Self-Illuminating Dot Systems and Methods of Use Thereof

ABSTRACT

Generally, aspects of the present disclosure are directed to conjugate systems, self-illuminating quantum dot conjugates, methods of detecting a target in a host, methods of treating a disease in a host, and the like.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of Ser. No. 12/159,150, filed on Jun.25, 2008, entitled “Self-Illuminating Dot Systems and Methods of UseThereof”, which claims priority to “Self-Illuminating Dot Systems andMethods of Use Thereof”, having serial number PCT/US2007/00096, filed onJan. 4, 2007. This application claims priority to the following U.S.provisional application: “Self-Illuminating Dot Systems and Methods ofUse Thereof,” having Ser. No. 60/756,591, filed on Jan. 4, 2006; whichis entirely incorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under contract CA114747awarded by the National Institutes of Health. The Government has certainrights in this invention.

BACKGROUND

Fluorescent semiconductor quantum dots (QDs) have generated wideinterest since their initial development and hold exciting potential formolecular imaging in living biological samples. Much of the excitementtowards QDs arises from their unique optical properties as fluorescenceimaging probes, as compared to traditional organic fluorophores, such ashigh quantum yield, high molar extinction coefficients, narrow emissionspectra, size-dependent tunable emission, and high photostability, allof which make QDs appealing for imaging living subjects. QDs fabricatedwith various coating molecules and functionalized with biomolecules suchas small peptides, proteins, antibodies, and nucleic acids, have beenemployed in a number of imaging studies. All reported QDs, however, needexcitation from external illumination sources in order to fluoresce,which often presents an inherent challenge in imaging opaque subjectssuch as small living animals. In biological tissues, there areubiquitous, endogenous chromophores such as collagens, porphyrins, andflavins, which are also excited by the illumination source and lead tosignificant background autofluorescence. In addition, short-wavelengthexcitation photons are largely scattered and absorbed in tissues,therefore, little light reaches and excites QDs present atnon-superficial locations.

SUMMARY

Generally, aspects of the present disclosure are directed to conjugatesystems, self-illuminating quantum dot conjugates, methods of detectinga target in a host, methods of treating a disease in a host, and thelike. Embodiments of the present disclosure include a conjugate system,among others, that includes: a self-illuminating quantum dot conjugatesystem that includes: a self-illuminating quantum dot conjugate and abioluminescence initiating compound, wherein the self-illuminatingquantum dot conjugate includes a bioluminescence donor molecule and aquantum dot, wherein the bioluminescence donor molecule and thebioluminescence initiating compound interact to produce abioluminescence energy, and wherein the quantum dot emits a fluorescenceenergy in response to the non-radiative transfer of the bioluminescenceenergy from the bioluminescence donor molecule to the quantum dot.

Embodiments of the present disclosure include a conjugate system, amongothers, that includes: a bioluminescence donor molecule and a quantumdot, wherein a bioluminescence energy is produced from thebioluminescence donor molecule, and wherein the quantum dot emits afluorescence energy in response to the non-radiative transfer of thebioluminescence energy from the bioluminescence donor molecule to thequantum dot.

Embodiments of the present disclosure include, among others, a method ofdetecting a target in a host that includes: providing aself-illuminating quantum dot conjugate, wherein the self-illuminatingquantum dot conjugate includes a bioluminescence donor molecule, aquantum dot, and at least one agent, wherein the agent has an affinityfor the target; introducing the self-illuminating quantum dot conjugateto a host; introducing a bioluminescence initiating compound to thehost; and determining the presence and location of the target in thehost corresponding to the agent by detecting the self-illuminatingquantum dot conjugate upon interaction with the bioluminescenceinitiating compound.

Embodiments of the present disclosure include, among others, treating adisease in a host among others, that includes: providing aself-illuminating quantum dot conjugate, wherein the self-illuminatingquantum dot conjugate includes a bioluminescence donor molecule, aquantum dot, and a first agent, wherein the first agent is effective attreating the disease; introducing the self-illuminating quantum dotconjugate to the subject in need for treatment of the disease;introducing a bioluminescence initiating compound to the host; anddetermining the location of the self-illuminating quantum dot conjugatein the host upon interaction with the bioluminescence initiatingcompound.

Embodiments of the present disclosure include, among others, a detectinga target in a host that includes: providing a self-illuminating quantumdot conjugate, wherein the self-illuminating quantum dot conjugateincludes a bioluminescence donor molecule, a quantum dot, and a firstagent, wherein the first agent is disposed between the quantum dot andthe bioluminescence donor molecule, and wherein the first agent isdegraded by a target; introducing the self-illuminating quantum dotconjugate to a host; introducing a bioluminescence initiating compoundto the host; detecting a fluorescent energy emitted from the quantumdot; and determining the presence of the target in the host by detectingthe decay of a fluorescent energy emitted from the quantum dot of theself-illuminating quantum dot conjugate upon degradation of the firstagent.

Embodiments of the present disclosure include a detecting a target in asystem, among others, that includes: providing a bioluminescence donormolecule complex and a quantum dot complex, wherein the bioluminescencedonor molecule complex includes a bioluminescence donor molecule,wherein the quantum dot complex includes a quantum dot; introducing eachof the bioluminescence donor molecule complex and the quantum dotcomplex independently to the system, wherein if the system includes thetarget, the target interacts with at least one of the bioluminescencedonor molecule complex or the quantum dot complex to cause thebioluminescence donor molecule complex and the quantum dot complex tobecome substantially close to one another; introducing a bioluminescenceinitiating compound to the system, wherein the bioluminescence donormolecule and the bioluminescence initiating compound interact to producea bioluminescence energy, and wherein the quantum dot emits afluorescence energy in response to the non-radiative transfer of thebioluminescence energy from the bioluminescence donor molecule to thequantum dot; and determining the presence of the target by detecting thefluorescent energy emitted from the quantum dot.

Embodiments of the present disclosure include a detecting a target in asystem, among others, that includes: providing a bioluminescence donormolecule complex and a quantum dot complex, wherein the bioluminescencedonor molecule complex includes a bioluminescence donor molecule,wherein the quantum dot complex includes a quantum dot, wherein one ofthe bioluminescence donor molecule complex or the quantum dot complexincludes a first agent that has an affinity for the first target,wherein the first target undergoes a change to a second target uponinteraction with the first agent, wherein the other of thebioluminescence donor molecule complex or the quantum dot complexincludes a second agent that has an affinity for the second target;introducing each of the bioluminescence donor molecule complex and thequantum dot complex independently to the system, wherein if the systemincludes the first target the first target undergoes a change to thesecond target upon interaction with the first agent, wherein thebioluminescence donor molecule complex and the quantum dot complexbecome substantially close to one another upon interaction of the thirdagent with the second target; introducing a bioluminescence initiatingcompound to the system, wherein the bioluminescence donor molecule andthe bioluminescence initiating compound interact to produce abioluminescence energy, and wherein the quantum dot emits a fluorescenceenergy in response to the non-radiative transfer of the bioluminescenceenergy from the bioluminescence donor molecule to the quantum dot; anddetermining the presence of the second target by detecting thefluorescent energy emitted from the quantum dot.

Embodiments of the present disclosure include a detecting a target in asystem, among others, that includes: providing a bioluminescence donormolecule complex and a quantum dot complex, wherein the bioluminescencedonor molecule complex includes a bioluminescence donor molecule,wherein the quantum dot complex includes a quantum dot, wherein one ofthe bioluminescence donor molecule complex or the quantum dot complexincludes a first agent that has an affinity for the first target,wherein the first agent undergoes a change to a second agent uponinteraction with the first target, wherein the other of thebioluminescence donor molecule complex or the quantum dot complexincludes a third agent that has an affinity for the second target;introducing each of the bioluminescence donor molecule complex and thequantum dot complex independently to the system, wherein if the systemincludes the first target the first agent undergoes a change to thesecond agent upon interaction with the first agent, wherein thebioluminescence donor molecule complex and the quantum dot complexbecome substantially close to one another upon interaction of the thirdagent with the second agent; introducing a bioluminescence initiatingcompound to the system, wherein the bioluminescence donor molecule andthe bioluminescence initiating compound interact to produce abioluminescence energy, and wherein the quantum dot emits a fluorescenceenergy in response to the non-radiative transfer of the bioluminescenceenergy from the bioluminescence donor molecule to the quantum dot; anddetermining the presence of the second target by detecting thefluorescent energy emitted from the quantum dot.

Other compositions, methods, features, and advantages of the presentdisclosure will be or become apparent to one with skill in the art uponexamination of the following drawings and detailed description. It isintended that all such additional compositions, methods, features, andadvantages be included within this description, be within the scope ofthe present disclosure, and be protected by the accompanying claims.

BRIEF DESCRIPTION OF THE DRAWINGS

Many aspects of the disclosure can be better understood with referenceto the following drawings. The components in the drawings are notnecessarily to scale, emphasis instead being placed upon clearlyillustrating the principles of the present disclosure. Moreover, in thedrawings, like reference numerals designate corresponding partsthroughout the several views.

FIG. 1 illustrates scheme 1, which shows the specific conjugation ofproteins to quantum dots mediated by the HaloTag protein and its ligand.

FIG. 2 illustrates scheme 2, which shows the synthesis of HaloTagligand 1. Reagent and conditions: a. Boc2O/EtOH, 0° C., 2 hr; b.NaH/DMF-THF and 6-chloro-1-iodohexane; c. TFA/anisole in DCM; d.NaH/DMF-THF and iodoacetic acid sodium salt; e. N-Hydroxysuccinimide andDCC in DCM; f. DIPEA/THF; and g. TFA/anisole in DCM.

FIGS. 3 a and 3 b illustrate the characterization of the size andfunction of the fusion protein. FIG. 3 a illustrates that the gelelectrophoresis analysis confirmed the size of HTP-Luc8. Both proteins(0.5 μg each) were run on a 4-12% Bis-Tris gradient denaturing gel andstained with Coomassie Blue. The expected sizes for Luc8 and HTP-Luc8were 37.1 and 70.3 kDa, respectively. FIG. 3 b illustrates thebioluminescence emission spectra of Luc8 (solid line) and HTP-Luc8 (dashline). The inset compares the total photon production of Luc8 andHTP-Luc8.

FIG. 4 illustrates the bioluminescence (black line) and fluorescence(dash grey line) spectra of conjugate QD@1-HTP-Luc8 in borate buffer.The fluorescence emission was collected with excitation at 480 nm.

FIGS. 5 and 6 illustrate the dependence of the conjugation on theligand 1. FIG. 5 illustrates a representative bioluminescence emissionspectra of the conjugate synthesized at different concentrations of 1(0, 20, 100, 500, 1000 and 2500 equivalents). FIG. 6 illustrates thetotal bioluminescence emissions from HTP-Luc8 and from quantum dots, andthe calculated BRET ratios of the conjugates prepared in FIG. 5 (induplicate).

FIG. 7 illustrates the bioluminescence emission spectra of quantum dotsconjugated with HTP-Luc8 (from top to bottom: 100, 50, 20, 10equivalents) or 20 equivalents of Luc8. The quantum dots were reactedwith 1000 equivalents of HaloTag ligand 1 before the conjugation withHTP-Luc8. Unconjugated proteins were removed by filtration beforemeasurement.

FIG. 8 illustrates the design and spectroscopic characterization ofself-illuminating QD conjugates based on BRET. FIG. 8 a illustrates aschematic of a QD that is covalently coupled to a BRET donor, Luc8. Thebioluminescence energy of Luc8-catalyzed oxidation of coelenterazine istransferred to the QDs, resulting in QD emission. FIG. 8 b illustratesthe absorption and emission spectra of QD655 (λex=480 nm), and spectrumof the bioluminescent light emitted in the oxidation of coelenterazinecatalyzed by Luc8. FIG. 8 c illustrates the gel electrophoresis analysisof the conjugation of Luc8 to QD655: (1) unconjugated QD655, (2) themixture of QD655 and the coupling reagent1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC), and(3) purified QD655-Luc8 conjugates. FIG. 8 d illustrates thebioluminescence emission spectrum of QD655-Luc8 in borate buffer. FIG. 8e illustrates the bioluminescence emission spectrum of QD655-Luc8 inmouse serum and in whole mouse blood.

FIG. 9 illustrates the bioluminescence and fluorescence imaging ofQD655-Luc8 and Luc8 injected subcutaneously (I and II) andintramuscularly (III and IV) at indicated sites in a living mouse (I andIII: QD655-Luc8, 5 pmol; II and IV: Luc8, 30 pmol): FIG. 9 a openwithout filters, and FIG. 9 b with 575-650 nm filter. FIG. 9 cillustrates the fluorescence imaging of the same mouse injected withindicated solutions in FIG. 9 a (excitation filter: 503-555 nm).

FIG. 10 illustrates multiplex imaging of conjugates QD605-Luc8,QD655-Luc8, QD705-Luc8, and QD800-Luc8 in vitro and in living mice. FIG.10 a illustrates the overlap of the bioluminescence emission of Luc8with the absorption spectra of QD605, QD655, QD705, and QD800. FIG. 10 billustrates fluorescence (λex=480 nm), and FIG. 10 c illustrates thebioluminescence emission spectra of indicated conjugates. FIG. 10 dillustrates the in vitro bioluminescence spectral imaging of solutionscontaining indicated conjugates. The image was collected for emissionfrom 580 to 850 nm. The different emissions are shown in pseudo colors.The sample at top left contained only Luc8, which showed no detectablelong-wavelength (580-850 nm) emission. FIG. 10 e illustrates the invitro bioluminescence spectral imaging of the same samples as in FIG. 10d, but images were collected at the indicated emission wavelength. FIGS.10 f-10 i illustrate the multiplex in vivo bioluminescence imaging ofthe following conjugates subcutaneously injected at indicated sites: (I)QD800-Luc8, 15 pmol; (II) QD705-Luc8, 15 pmol; (III) a mixture ofQD655-Luc8, QD705-Luc8, and QD800-Luc8; and (IV) QD655-Luc8, 5 pmol.Images were collected with the following emission filters: FIG. 10 fwithout any filter, FIG. 10 g with 575-650 nm filter, FIG. 10 h withx-Cy5.5 filter (680-720 nm), and FIG. 10 i with ICG filter (810-875 nm).The acquisition time was 2 min.

FIG. 11 illustrates the imaging of C6 glioma cells labeled withQD655-Luc8-R9 in vitro and in living mice. FIG. 11 a illustrates theoverlay of fluorescence and differential interference contrast (DIC)images of QD655-Luc8-R9 labeled C6 glioma cells. Fluorescence image wascollected with the following filter set (Chroma Technology Corporation,Vermont): excitation, 420/40; emission, D660/40; dichroic, 475DCXR.Scale bar: 50 μm. FIG. 11 b illustrates representative bioluminescenceimages of labeled cells acquired with a filter (575-650 nm) (left) andwithout any filter (right). FIG. 11 c illustrates representativebioluminescence images of a nude mouse injected via tail vein withlabeled cells, acquired with a filter (575-650 nm) (left) and withoutany filter (right). FIG. 11 d illustrates a fluorescence image of thesame mouse in FIG. 11 c (Excitation filter: 503-555 nm). FIG. 11 eillustrates an overlay of fluorescence and DIC images of a lung slice ofthe same mouse imaged in FIG. 11 c, and FIG. 11 d shows the accumulationof QD conjugates in the lungs; the same filter set as in FIG. 11 a wasused. Scale bar: 50 μm.

FIG. 12 illustrates the dependence of the BRET efficiency on thedistance between QDs and Luc8's. FIG. 12 a illustrates a schematic oftwo conjugates with different size: a covalent conjugate with Luc8directly coupled to QD655 (20 nm), and a non-covalent complex with Luc8binding to a streptavidin-coated QD655a (22 nm) meditated by abiotinylated NTA ligand. FIG. 12 b illustrates the fluorescence spectraof two complexes at equal concentrations (5.5 pmol). FIG. 12 cillustrates the bioluminescence emission spectra of two complexes atequal concentrations upon the addition of 1 μg coelenterazine.

FIG. 13 illustrates the effect of the number of immobilized Luc8 on theBRET efficiency of QD655-Luc8 conjugates. FIG. 13 a illustrates thebioluminescence emission spectra of QD655-Luc8 conjugates prepared atindicated QD655/Luc8 ratios. FIG. 13 b illustrates the gelelectrophoresis analysis of indicated QD655-Luc8 conjugates. FIG. 13 cillustrates the BRET ratio of indicated conjugates calculated from theiremission spectra in FIG. 13 a.

FIG. 14 illustrates bioluminescence and fluorescence imaging ofQD655-Luc8 and Luc8 injected subcutaneously (I and II) andintramuscularly (III and IV) at indicated sites in a living mouse (I andIII: QD655-Luc8, 5 pmol; II and IV: Luc8, 30 pmol). FIG. 14 a openwithout filters, and FIG. 14 b with 650-660 nm filter. FIG. 14 cillustrates fluorescence imaging of the same mouse injected withindicated solutions in FIG. 14 a (excitation filter: 503-555 nm).

FIG. 15 illustrates a schematic for BRET-based detection of MMP-2 withNanosensors.

FIG. 16 is a luminescence spectra of the mixture of QD655@COOH (50 nM)and Luc8-6xHis fusion protein (400 nM) containing 1) No Ni²⁺, 2) Ni²⁺(100 μM), 3) Ni²⁺ (100 μM) and EDTA (200 μM), and 4) Ni²⁺ (100 μM) andimidazole (300 mM).

FIG. 17 illustrates the detection of MMP-2 with the BRET-based QDnanosensors.

FIG. 17A illustrates a representative bioluminescence emission spectraof the mixture containing QD655@COOH (40 nM), Ni²⁺ (100 μM), and theLuc8 fusion protein (16 μM) incubated with MMP-2 (10 μg/mL) at theindicated periods of time. FIG. 17B illustrates a plot of the BRET ratiovs. time for indicated MMP-2 concentrations.

FIG. 18 illustrates MMP-2 cleavage of the Luc8 fusion protein. FIG. 18Aillustrates a NuPAGE assay. Lane 1 is the fusion Luc8 protein (size:37.6 kD). Lane 2 is a MMP-2 treated fusion Luc8 protein (size 36.5 kD).Lane 3 is a mixture of 1 and 2. FIG. 18B illustrates a bioluminescenceemission of the fusion protein before and after MMP-2 cleavage.

FIG. 19 illustrates the luminescence spectra of QD655@COOH (solid line)and QD655@NH₂ (dashed line) in the presence of 100 μM of Ni²⁺ and 400 nMof Luc8 fusion protein.

FIG. 20 illustrates the dependence of the BRET emission on the [Ni²⁺]with representative bioluminescence spectra of the mixture containingQD655@COOH (20 nM), the fusion protein (640 nM) and differentconcentrations of Ni²⁺ (0, 2, 4, 6, 10, 20, 40, 80, and 100 μM).

FIG. 21 illustrates a schematic of the PKA detection based on theformation of the self-Illuminating complex mediated by the PKAphosphorylation.

FIG. 22 illustrates the detection of the PKA by QD BRET sensor.

DETAILED DESCRIPTION

Before the present disclosure is described in greater detail, it is tobe understood that this disclosure is not limited to particularembodiments described, and as such may, of course, vary. It is also tobe understood that the terminology used herein is for the purpose ofdescribing particular embodiments only, and is not intended to belimiting, since the scope of the present disclosure will be limited onlyby the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range, is encompassed within the disclosure. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges and are also encompassed within the disclosure, subjectto any specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either orboth of those included limits are also included in the disclosure.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present disclosure, the preferredmethods and materials are now described.

All publications and patents cited in this specification are hereinincorporated by reference as if each individual publication or patentwere specifically and individually indicated to be incorporated byreference and are incorporated herein by reference to disclose anddescribe the methods and/or materials in connection with which thepublications are cited. The citation of any publication is for itsdisclosure prior to the filing date and should not be construed as anadmission that the present disclosure is not entitled to antedate suchpublication by virtue of prior disclosure. Further, the dates ofpublication provided could be different from the actual publicationdates that may need to be independently confirmed.

As will be apparent to those of skill in the art upon reading thisdisclosure, each of the individual embodiments described and illustratedherein has discrete components and features which may be readilyseparated from or combined with the features of any of the other severalembodiments without departing from the scope or spirit of the presentdisclosure. Any recited method can be carried out in the order of eventsrecited or in any other order that is logically possible.

Embodiments of the present disclosure will employ, unless otherwiseindicated, techniques of synthetic organic chemistry, biochemistry,biology, molecular biology, recombinant DNA techniques, pharmacology,and the like, which are within the skill of the art. Such techniques areexplained fully in the literature. In particular, See, e.g., Maniatis,Fritsch & Sambrook, “Molecular Cloning: A Laboratory Manual (1982); “DNACloning: A Practical Approach,” Volumes I and II (D. N. Glover ed.1985); “Oligonucleotide Synthesis” (M. J. Gait ed. 1984); “Nucleic AcidHybridization” (B. D. Hames & S. J. Higgins eds. (1985)]; “Transcriptionand Translation” (B. D. Hames & S. J. Higgins eds. (1984)); “Animal CellCulture” (R. I. Freshney, ed. (1986)); “Immobilized Cells and Enzymes”(IRL Press, (1986)); B. Perbal, “A Practical Guide To Molecular Cloning”(1984), each of which is incorporated herein by reference.

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how toperform the methods and use the compositions and compounds disclosed andclaimed herein. Efforts have been made to ensure accuracy with respectto numbers (e.g., amounts, temperature, etc.), but some errors anddeviations should be accounted for. Unless indicated otherwise, partsare parts by weight, temperature is in ° C., and pressure is at or nearatmospheric. Standard temperature and pressure are defined as 20° C. and1 atmosphere.

Before the embodiments of the present disclosure are described indetail, it is to be understood that, unless otherwise indicated, thepresent disclosure is not limited to particular materials, reagents,reaction materials, manufacturing processes, or the like, as such canvary. It is also to be understood that the terminology used herein isfor purposes of describing particular embodiments only, and is notintended to be limiting. It is also possible in the present disclosurethat steps can be executed in different sequence where this is logicallypossible.

It must be noted that, as used in the specification and the appendedclaims, the singular forms “a,” “an,” and “the” include plural referentsunless the context clearly dictates otherwise. Thus, for example,reference to “a compound” includes a plurality of compounds. In thisspecification and in the claims that follow, reference will be made to anumber of terms that shall be defined to have the following meaningsunless a contrary intention is apparent.

DEFINITIONS

In describing and claiming the disclosed subject matter, the followingterminology will be used in accordance with the definitions set forthbelow.

“Bioluminescent donor protein” refers to a protein capable of acting ona bioluminescent initiator molecule substrate to generatebioluminescence.

“Bioluminescent initiator molecule” is a molecule that can react with abioluminescent donor protein to generate bioluminescence.

Bioluminescence (BL) is defined as emission of light by living organismsthat is well visible in the dark and affects visual behavior of animals(See e.g., Harvey, E. N. (1952). Bioluminescence. New York: AcademicPress; Hastings, J. W. (1995). Bioluminescence. In: Cell Physiology (ed.by N. Speralakis). pp. 651-681. New York: Academic Press.; Wilson, T.and Hastings, J. W. (1998). Bioluminescence. Annu Rev Cell Dev Biol 14,197-230.). Bioluminescence does not include so-called ultra-weak lightemission, which can be detected in virtually all living structures usingsensitive luminometric equipment (Murphy, M. E. and Sies, H. (1990),Meth. Enzymol. 186, 595-610; Radotic, K, Radenovic, C, Jeremic, M.(1998), Gen Physiol Biophys 17, 289-308). Bioluminescence also does notinclude weak light emissions, which most probably do not play anyecological role, such as the glowing of bamboo growth cone (Totsune, H.,Nakano, M., Inaba, H. (1993), Biochem. Biophys. Res Comm. 194,1025-1029). Bioluminescence also does not include emission of lightduring fertilization of animal eggs (Klebanoff, S. J., Froeder, C. A.,Eddy, E. M., Shapiro, B. M. (1979), J. Exp. Med. 149, 938-953; Schomer,B. and Epel, D. (1998), Dev Biol 203, 1-11). Each of the citationsreferenced above are incorporated herein by reference.

The term “polymer” means any compound that is made up of two or moremonomeric units covalently bonded to each other, where the monomericunits may be the same or different, such that the polymer may be ahomopolymer or a heteropolymer. Representative polymers includepeptides, polysaccharides, nucleic acids and the like, where thepolymers may be naturally occurring or synthetic.

The term “polypeptides” includes proteins and fragments thereof.Polypeptides are disclosed herein as amino acid residue sequences. Thosesequences are written left to right in the direction from the amino tothe carboxy terminus. In accordance with standard nomenclature, aminoacid residue sequences are denominated by either a three letter or asingle letter code as indicated as follows: Alanine (Ala, A), Arginine(Arg, R), Asparagine (Asn, N), Aspartic Acid (Asp, D), Cysteine (Cys,C), Glutamine (Gln, Q), Glutamic Acid (Glu, E), Glycine (Gly, G),Histidine (His, H), Isoleucine (Ile, I), Leucine (Leu, L), Lysine (Lys,K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P),Serine (Ser, S), Threonine (Thr, T), Tryptophan (Trp, W), Tyrosine (Tyr,Y), and Valine (Val, V). In addition, the protein can includenon-standard and/or non-naturally occurring amino acids, as well asother amino acids that may be found in phosphorylated proteins inorganisms such as, but not limited to, animals, plants, insects,protists, fungi, bacteria, algae, single-cell organisms, and the like.The non-standard amino acids include, but are not limited to,selenocysteine, pyrrolysine, gamma-aminobutyric acid, carnitine,ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine,sarcosine, and the like. The non-naturally occurring amino acidsinclude, but are not limited to, trans-3-methylproline,2,4-methanoproline, cis-4-hydroxyproline, trans-4-hydroxyproline,N-methyl-glycine, allo-threonine, methylthreonine,hydroxy-ethylcysteine, hydroxyethylhomocysteine, nitro-glutamine,homoglutamine, pipecolic acid, thiazolidine carboxylic acid,dehydroproline, 3- and 4-methylproline, 3,3-dimethylproline,tert-leucine, norvaline, 2-azaphenylalanine, 3-azaphenylalanine,4-azaphenylalanine, and 4-fluorophenylalanine.

“Variant” refers to a polypeptide or polynucleotide that differs from areference polypeptide or polynucleotide, but retains essentialproperties. A typical variant of a polypeptide differs in amino acidsequence from another, reference polypeptide. Generally, differences arelimited so that the sequences of the reference polypeptide and thevariant are closely similar overall and, in many regions, identical. Avariant and reference polypeptide may differ in amino acid sequence byone or more modifications (e.g., substitutions, additions, and/ordeletions). A variant of a polypeptide includes conservatively modifiedvariants. A substituted or inserted amino acid residue may or may not beone encoded by the genetic code. A variant of a polypeptide may benaturally occurring, such as an allelic variant, or it may be a variantthat is not known to occur naturally.

Modifications and changes can be made in the structure of thepolypeptides of this disclosure and still obtain a molecule havingsimilar characteristics as the polypeptide (e.g., a conservative aminoacid substitution). For example, certain amino acids can be substitutedfor other amino acids in a sequence without appreciable loss ofactivity. Because it is the interactive capacity and nature of apolypeptide that defines that polypeptide's biological functionalactivity, certain amino acid sequence substitutions can be made in apolypeptide sequence and nevertheless obtain a polypeptide with likeproperties.

In making such changes, the hydropathic index of amino acids can beconsidered. The importance of the hydropathic amino acid index inconferring interactive biologic function on a polypeptide is generallyunderstood in the art. It is known that certain amino acids can besubstituted for other amino acids having a similar hydropathic index orscore and still result in a polypeptide with similar biologicalactivity. Each amino acid has been assigned a hydropathic index on thebasis of its hydrophobicity and charge characteristics. Those indicesare: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine(+2.8); cysteine/cysteine (+2.5); methionine (+1.9); alanine (+1.8);glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9);tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5);glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9);and arginine (−4.5).

It is believed that the relative hydropathic character of the amino aciddetermines the secondary structure of the resultant polypeptide, whichin turn defines the interaction of the polypeptide with other molecules,such as enzymes, substrates, receptors, antibodies, antigens, and thelike. It is known in the art that an amino acid can be substituted byanother amino acid having a similar hydropathic index and still obtain afunctionally equivalent polypeptide. In such changes, the substitutionof amino acids whose hydropathic indices are within ±2 is preferred,those within ±1 are particularly preferred, and those within ±0.5 areeven more particularly preferred.

Substitution of like amino acids can also be made on the basis ofhydrophilicity, particularly, where the biological functional equivalentpolypeptide or peptide thereby created is intended for use inimmunological embodiments. The following hydrophilicity values have beenassigned to amino acid residues: arginine (+3.0); lysine (+3.0);aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine(+0.2); glutamine (+0.2); glycine (0); proline (−0.5±1); threonine(−0.4); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine(−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine(−2.3); phenylalanine (−2.5); tryptophan (−3.4). It is understood thatan amino acid can be substituted for another having a similarhydrophilicity value and still obtain a biologically equivalent, and inparticular, an immunologically equivalent polypeptide. In such changes,the substitution of amino acids whose hydrophilicity values are within±2 is preferred, those within ±1 are particularly preferred, and thosewithin ±0.5 are even more particularly preferred.

As outlined above, amino acid substitutions are generally based on therelative similarity of the amino acid side-chain substituents, forexample, their hydrophobicity, hydrophilicity, charge, size, and thelike. Exemplary substitutions that take various of the foregoingcharacteristics into consideration are well known to those of skill inthe art and include (original residue: exemplary substitution): (Ala:Gly, Ser), (Arg: Lys), (Asn: Gln, His), (Asp: Glu, Cys, Ser), (Gln:Asn), (Glu: Asp), (Gly: Ala), (His: Asn, Gln), (Ile: Leu, Val), (Leu:Ile, Val), (Lys: Arg), (Met: Leu, Tyr), (Ser: Thr), (Thr: Ser), (Tip:Tyr), (Tyr: Trp, Phe), and (Val: Ile, Leu). Embodiments of thisdisclosure thus contemplate functional or biological equivalents of apolypeptide as set forth above. In particular, embodiments of thepolypeptides can include variants having about 50%, 60%, 70%, 80%, 90%,and 95% sequence identity to the polypeptide of interest.

“Identity,” as known in the art, is a relationship between two or morepolypeptide sequences, as determined by comparing the sequences. In theart, “identity” also means the degree of sequence relatedness betweenpolypeptides as determined by the match between strings of suchsequences. “Identity” and “similarity” can be readily calculated byknown methods, including, but not limited to, those described in(Computational Molecular Biology, Lesk, A. M., Ed., Oxford UniversityPress, New York, 1988; Biocomputing: Informatics and Genome Projects,Smith, D. W., Ed., Academic Press, New York, 1993; Computer Analysis ofSequence Data, Part I, Griffin, A. M., and Griffin, H. G., Eds., HumanaPress, New Jersey, 1994; Sequence Analysis in Molecular Biology, vonHeinje, G., Academic Press, 1987; and Sequence Analysis Primer,Gribskov, M. and Devereux, J., Eds., M Stockton Press, New York, 1991;and Carillo, H., and Lipman, D., SIAM J Applied Math., 48: 1073 (1988).

Preferred methods to determine identity are designed to give the largestmatch between the sequences tested. Methods to determine identity andsimilarity are codified in publicly available computer programs. Thepercent identity between two sequences can be determined by usinganalysis software (e.g., Sequence Analysis Software Package of theGenetics Computer Group, Madison Wis.) that incorporates the Needelmanand Wunsch, (J. Mol. Biol., 48: 443-453, 1970) algorithm (e.g., NBLAST,and XBLAST). The default parameters are used to determine the identityfor the polypeptides of the present disclosure.

By way of example, a polypeptide sequence may be identical to thereference sequence, that is 100% identical, or it may include up to acertain integer number of amino acid alterations as compared to thereference sequence such that the % identity is less than 100%. Suchalterations are selected from: at least one amino acid deletion,substitution, including conservative and non-conservative substitution,or insertion, and wherein said alterations may occur at the amino- orcarboxy-terminal positions of the reference polypeptide sequence oranywhere between those terminal positions, interspersed eitherindividually among the amino acids in the reference sequence or in oneor more contiguous groups within the reference sequence. The number ofamino acid alterations for a given % identity is determined bymultiplying the total number of amino acids in the reference polypeptideby the numerical percent of the respective percent identity (divided by100) and then subtracting that product from said total number of aminoacids in the reference polypeptide.

Conservative amino acid variants can also comprise non-naturallyoccurring amino acid residues. Non-naturally occurring amino acidsinclude, without limitation, trans-3-methylproline, 2,4-methanoproline,cis-4-hydroxyproline, trans-4-hydroxyproline, N-methyl-glycine,allo-threonine, methylthreonine, hydroxy-ethylcysteine,hydroxyethylhomocysteine, nitro-glutamine, homoglutamine, pipecolicacid, thiazolidine carboxylic acid, dehydroproline, 3- and4-methylproline, 3,3-dimethylproline, tert-leucine, norvaline,2-azaphenyl-alanine, 3-azaphenylalanine, 4-azaphenylalanine, and4-fluorophenylalanine. Several methods are known in the art forincorporating non-naturally occurring amino acid residues into proteins.For example, an in vitro system can be employed wherein nonsensemutations are suppressed using chemically aminoacylated suppressortRNAs. Methods for synthesizing amino acids and aminoacylating tRNA areknown in the art. Transcription and translation of plasmids containingnonsense mutations is carried out in a cell-free system comprising an E.coli S30 extract and commercially available enzymes and other reagents.Proteins are purified by chromatography. (Robertson, et al., J. Am.Chem. Soc., 113: 2722, 1991; Ellman, et al., Methods Enzymol., 202: 301,1991; Chung, et al., Science, 259: 806-9, 1993; and Chung, et al., Proc.Natl. Acad. Sci. USA, 90: 10145-9, 1993). In a second method,translation is carried out in Xenopus oocytes by microinjection ofmutated mRNA and chemically aminoacylated suppressor tRNAs (Turcatti, etal., J. Biol. Chem., 271: 19991-8, 1996). Within a third method, E. colicells are cultured in the absence of a natural amino acid that is to bereplaced (e.g., phenylalanine) and in the presence of the desirednon-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine,3-azaphenylalanine, 4-azaphenylalanine, or 4-fluorophenylalanine). Thenon-naturally occurring amino acid is incorporated into the protein inplace of its natural counterpart. (Koide, et al., Biochem., 33: 7470-6,1994). Naturally occurring amino acid residues can be converted tonon-naturally occurring species by in vitro chemical modification.Chemical modification can be combined with site-directed mutagenesis tofurther expand the range of substitutions (Wynn, et al., Protein Sci.,2: 395-403, 1993).

As used herein, the term “polynucleotide” generally refers to anypolyribonucleotide or polydeoxyribonucleotide, which may be unmodifiedRNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotidesas used herein refers to, among others, single- and double-stranded DNA,DNA that is a mixture of single- and double-stranded regions, single-and double-stranded RNA, and RNA that is mixture of single- anddouble-stranded regions, hybrid molecules comprising DNA and RNA thatmay be single-stranded or, more typically, double-stranded or a mixtureof single- and double-stranded regions. Polynucleotide encompasses theterms “nucleic acid,” “nucleic acid sequence,” or “oligonucleotide” asdefined above.

In addition, polynucleotide as used herein refers to triple-strandedregions comprising RNA or DNA or both RNA and DNA. The strands in suchregions may be from the same molecule or from different molecules. Theregions may include all of one or more of the molecules, but moretypically involve only a region of some of the molecules. One of themolecules of a triple-helical region often is an oligonucleotide.

As used herein, the term polynucleotide includes DNAs or RNAs asdescribed above that contain one or more modified bases. Thus, DNAs orRNAs with backbones modified for stability or for other reasons are“polynucleotides” as that term is intended herein. Moreover, DNAs orRNAs comprising unusual bases, such as inosine, or modified bases, suchas tritylated bases, to name just two examples, are polynucleotides asthe term is used herein.

It will be appreciated that a great variety of modifications have beenmade to DNA and RNA that serve many useful purposes known to those ofskill in the art. The term polynucleotide as it is employed hereinembraces such chemically, enzymatically or metabolically modified formsof polynucleotides, as well as the chemical forms of DNA and RNAcharacteristic of viruses and cells, including simple and complex cells,inter alias.

By way of example, a polynucleotide sequence of the present disclosuremay be identical to the reference sequence, that is be 100% identical,or it may include up to a certain integer number of nucleotidealterations as compared to the reference sequence. Such alterations areselected from the group including at least one nucleotide deletion,substitution, including transition and transversion, or insertion, andwherein said alterations may occur at the 5′ or 3′ terminal positions ofthe reference nucleotide sequence or anywhere between those terminalpositions, interspersed either individually among the nucleotides in thereference sequence or in one or more contiguous groups within thereference sequence. The number of nucleotide alterations is determinedby multiplying the total number of nucleotides in the referencenucleotide by the numerical percent of the respective percent identity(divided by 100) and subtracting that product from said total number ofnucleotides in the reference nucleotide. Alterations of a polynucleotidesequence encoding the polypeptide may alter the polypeptide encoded bythe polynucleotide following such alterations.

The term “codon” means a specific triplet of mononucleotides in the DNAchain. Codons correspond to specific amino acids (as defined by thetransfer RNAs) or to start and stop of translation by the ribosome.

The term “degenerate nucleotide sequence” denotes a sequence ofnucleotides that includes one or more degenerate codons (as compared toa reference polynucleotide molecule that encodes a polypeptide).Degenerate codons contain different triplets of nucleotides, but encodethe same amino acid residue (e.g., GAU and GAC triplets each encodeAsp).

As used herein, the terms “host” or “organism” include humans, mammals(e.g., cats, dogs, horses, etc.), living cells, and other livingorganisms, as well as samples such as tissue taken from a host ororganism. A living organism can be as simple as, for example, a singleeukaryotic cell or as complex as a mammal.

General Discussion

Embodiments of the present disclosure include conjugate systems, methodsof using conjugate systems, self-illuminating quantum dot conjugates,systems including self-illuminating quantum dot conjugates, methods ofusing the self-illuminating quantum dot conjugates, and the like. Ingeneral, embodiments of the present disclosure involve the non-radiativetransfer of energy between a bioluminescence donor molecule and aquantum dot without external illumination. In general, thebioluminescence donor molecule interacts with a bioluminescenceinitiating molecule to produce an emission. The non-radiative transferof energy from the bioluminescence donor molecule to the quantum dotscauses the quantum dot to emit radiation at a different wavelength thatcan be detected and measured using an appropriate detection system. Inother words, bioluminescence resonance energy transfer (BRET) can takeplace between the bioluminescence donor molecule and the quantum dot. Inthis regard, embodiments of the present disclosure do not need anexternal light source to produce an emission from the quantum dot.

The conjugate (e.g., self-illuminating quantum dot conjugate) can beused to produce bioluminescent and/or fluorescent images. In addition,multiplexed imaging of one or more targets can be performed by using aplurality of self-illuminating quantum dot conjugates where eachconjugate includes a quantum dot with distinct emission spectra.Further, embodiments of the present disclosure can producebioluminescence at relatively longer wavelengths than currently used,which provides methods and systems of imaging in deep tissues.

It should also be noted that since the self-illuminating quantum dotconjugate does not need an external illumination source, the sensitivityis increased because the background signal-to-noise ratio increases. Itshould also be noted that the endogenous chromophores in the imagedtissue do not emit radiation in response to an external illuminationsource, where such radiation would decrease the signal-to-noise ratio.

In addition, the self-illuminating quantum dot conjugates aredistinguishable and can be individually detected. In this regard, theself-illuminating quantum dot conjugates can be modified so that theself-illuminating quantum dot conjugates interact with certain targetsor target compounds (e.g., chemical and/or biological compounds orpolymers such a biomolecules, proteins, DNA, RNA, and the like), whichallows detection of the target molecules (e.g., in-vivo) therebydetermining the area in which the target molecules are located, forexample. In an embodiment, the target can include, but is not limitedto, a compound, a polypeptide, a polynucleotide, an antibody, anantigen, a hapten, a cell type, a tissue type, an agent (as describedbelow), and the like

Embodiments of the disclosure can be used in applications such as thefollowing: cellular studies, in vivo cell trafficking, stem cellstudies, tumor imaging, biomolecule array systems, biosensing,biolabeling, gene expression studies, protein studies, medicaldiagnostics, diagnostic libraries, microfluidic systems, deliveryvehicles, multiplex imaging of multiple events substantiallysimultaneously, and high throughput assays for drug screening. Forexample, the self-illuminating quantum dot conjugates in combinationwith spectral imaging can be used for multiplexed imaging and detection(in vitro or in vivo) of polynucleotides, polypeptides, and the like, ina system, a host or single living cells. The self-illuminating quantumdot conjugates can be used to detect (and visualize) and quantitateevents in a system, a host or a cell in in vitro as well as in in vivostudies, which decreases time and expenses since the same system can beused for cells and living organisms. For example, a drug being tested incell culture with the self-illuminating quantum dot conjugates can thenalso be tested in living subjects using the same self-illuminatingquantum dot conjugates.

Embodiments of the disclosure can be used to non-invasively measureselected events or interactions, the presence or absence of an agent(e.g., chemical and/or biological compounds or polymers), and the likeat a depth in an animal from about less than 6 centimeters (cm), lessthan about 5 cm, less than about 4 cm, less than about 3 cm, less thanabout 2 cm, and less than about 1 cm. For example, the self-illuminatingquantum dot conjugates can be used to measure cellular events in deeptissue.

In particular, the self-illuminating quantum dot conjugates can be usedin in-vivo diagnostic and/or therapeutic applications such as, but notlimited to, targeting diseases and/or conditions and/or imaging diseasesand/or conditions. For example, one or more embodiments of theself-illuminating quantum dot conjugates can be used to identify thetype of disease, locate the proximal locations of the disease, and/ordeliver agents (e.g, drugs) to the diseased cells (e.g., cancer cells,tumors, and the like) in living animals.

As mentioned above, the self-illuminating quantum dot conjugate includesa bioluminescence donor molecule and a quantum dot. In the presence ofthe bioluminescence initiating molecule or compound, the bioluminescenceinitiating compound can react with the bioluminescence donor molecule.The reaction causes the bioluminescence donor molecule to emitbioluminescence energy. The non-radiative energy transfer from thebioluminescence donor molecule to the quantum dot can occur when thereis an overlap (e.g., greater than 0.1%) between the emission andexcitation spectra of the donor and acceptor molecules, respectively. Itshould be noted that the greater the overlap, the greater theefficiency. The energy is accepted by the quantum dot, and then thequantum dot emits fluorescent energy. The bioluminescence energy and/orthe fluorescent energy can be detected and quantified in real time usingan appropriate detection system (e.g., a photomultiplier tube in afluorometer and/or a luminometer, for example).

In an embodiment, the self-illuminating quantum dot conjugate could bedesigned to degrade in the presence of certain agents. Therefore, theratio of the bioluminescence energy and the fluorescent energy can bedetected and quantified in real time to watch the self-illuminatingquantum dot conjugate degrade. Thus, the presence of an agent (e.g., anagent present in a precancerous cell, cancer, and/or tumor, or someother disease) can be detected by observing the decay of the fluorescentenergy emitted by the quantum dot because the BRET between the quantumdot and the bioluminescence donor molecule is reduced and/or eliminated.

In another embodiment, a conjugate system includes a bioluminescencedonor molecule complex and a quantum dot complex. The bioluminescencedonor molecule complex and the quantum dot complex are introduced to thesystem independently (e.g., as two separate complexes). Thebioluminescence donor molecule complex includes a bioluminescence donormolecule, while the quantum dot complex includes a quantum dot. A targetof interest modifies or combines with either the bioluminescence donormolecule complex or the quantum dot complex causing the two complexes tocome in substantially close proximity (e.g., about 50 to 100 Angstroms),which would allow non-radiative energy transfer from the bioluminescencedonor molecule to the quantum dot in the presence of the bioluminescenceinitiating molecule or compound. The term “substantially closeproximity” includes distances that allow for non-radiative energytransfer from the bioluminescence donor molecule to the quantum dot inthe presence of the bioluminescence initiating molecule or compound. Inan embodiment, the complexes may associate with one another and remainas two separate complexes. In another embodiment, the complexes may selfassemble into a single complex (e.g., a stable complex or one that coulddegrade under appropriate conditions such as those described herein). Inanother embodiment, the two complexes can form a single complex. Theresulting bioluminescence donor molecule/quantum dot conjugate may be astable molecule, or an entity that degrades with time or an externalstimuli such as the presence of a chemical agent or a change in thesurrounding environment that degrades the entity.

The reaction of the bioluminescence initiating molecule with thebioluminescence donor molecule causes the bioluminescence donor moleculeto emit bioluminescence energy. The non-radiative energy transfer fromthe bioluminescence donor molecule to the quantum dot can occur whenthere is an overlap (e.g., greater than 0.1%) between the emission andexcitation spectra of the donor and acceptor molecules, respectively.The energy is accepted by the quantum dot, and then the quantum dotemits fluorescent energy. The bioluminescence energy and/or thefluorescent energy can be detected and quantified in real time (e.g., invivo or in vitro) using an appropriate detection system.

For example, a conjugate system includes a bioluminescence donormolecule complex and a quantum dot complex. The bioluminescence donormolecule complex and the quantum dot complex are introduced to thesystem independently (e.g., as two separate complexes). Thebioluminescence donor molecule complex includes a bioluminescence donormolecule, while the quantum dot complex includes a quantum dot. One ofthe bioluminescence donor molecule complex or the quantum dot complexincludes a first agent (e.g., protein) that has an affinity for a firsttarget (e.g., protein). Upon interaction with the first agent, the firsttarget undergoes a change to a second target (still having an affinityfor the first agent or otherwise bound to the complex). The other of thebioluminescence donor molecule complex or the quantum dot complexincludes a second agent that has an affinity for the second target sothat the two complexes are attracted to one another. In other words,when one of the agents of a first complex interacts with a target ofinterest, the target undergoes a chemical, biological, and/or physicalchange. The second complex (other complex) includes an agent that has anaffinity for the target after the chemical, biological, and/or physicalchange, so that the two complexes are attracted to one another.

The interaction causes the two complexes to come in substantially closeproximity (e.g., 50 to 100 Angstroms), which would allow non-radiativeenergy transfer from the bioluminescence donor molecule to the quantumdot in the presence of the bioluminescence initiating molecule orcompound. The term “substantially close proximity” includes distancesthat allow for non-radiative energy transfer from the bioluminescencedonor molecule to the quantum dot in the presence of the bioluminescenceinitiating molecule or compound.

The reaction of the bioluminescence initiating molecule with thebioluminescence donor molecule causes the bioluminescence donor moleculeto emit bioluminescence energy. The non-radiative energy transfer fromthe bioluminescence donor molecule to the quantum dot can occur whenthere is an overlap (e.g., greater than 0.1%) between the emission andexcitation spectra of the donor and acceptor molecules, respectively.The energy is accepted by the quantum dot, and then the quantum dotemits fluorescent energy. The bioluminescence energy and/or thefluorescent energy can be detected and quantified in real time (e.g., invivo or in vitro) using an appropriate detection system.

In another example, a conjugate system includes a bioluminescence donormolecule complex and a quantum dot complex. The bioluminescence donormolecule complex and the quantum dot complex are introduced to thesystem independently (e.g., as two separate complexes). Thebioluminescence donor molecule complex includes a bioluminescence donormolecule, while the quantum dot complex includes a quantum dot. One ofthe bioluminescence donor molecule complex or the quantum dot complexincludes a first agent (e.g., protein) that has an affinity for a firsttarget (e.g., protein). Upon interaction with first target, the firstagent undergoes a change to a second agent. The other of thebioluminescence donor molecule complex or the quantum dot complexincludes a third agent that has an affinity for the second agent so thatthe two complexes are attracted to one another. In other words, when oneof the agents of a first complex interacts with a target of interest,the agent or first complex undergoes a chemical, biological, and/orphysical change. The second complex (other complex) includes an agentthat has an affinity for the agent of the first complex or the firstcomplex after the chemical, biological, and/or physical change, so thatthe two complexes are attracted to one another.

The interaction causes the two complexes to come in substantially closeproximity (e.g., 50 to 100 Angstroms), which would allow non-radiativeenergy transfer from the bioluminescence donor molecule to the quantumdot in the presence of the bioluminescence initiating molecule orcompound. The term “substantially close proximity” includes distancesthat allow for non-radiative energy transfer from the bioluminescencedonor molecule to the quantum dot in the presence of the bioluminescenceinitiating molecule or compound.

The reaction of the bioluminescence initiating molecule with thebioluminescence donor molecule causes the bioluminescence donor moleculeto emit bioluminescence energy. The non-radiative energy transfer fromthe bioluminescence donor molecule to the quantum dot can occur whenthere is an overlap (e.g., greater than about 0.1%) between the emissionand excitation spectra of the donor and acceptor molecules,respectively. The energy is accepted by the quantum dot, and then thequantum dot emits fluorescent energy. The bioluminescence energy and/orthe fluorescent energy can be detected and quantified in real time(e.g., in vivo or in vitro) using an appropriate detection system.

In another example, a conjugate system includes a bioluminescence donormolecule complex and a quantum dot complex. The bioluminescence donormolecule complex and the quantum dot complex are introduced to thesystem independently (e.g., as two separate complexes). Thebioluminescence donor molecule complex includes a bioluminescence donormolecule, while the quantum dot complex includes a quantum dot. One ofthe bioluminescence donor molecule complex or the quantum dot complexincludes a first agent (e.g., protein) that has an affinity for a firsttarget (e.g., protein). Upon interaction with a second agent, the firsttarget undergoes a change (e.g., chemical, biological, and/or physicalchange) to a second target (still having an affinity for the firstagent). The other of the bioluminescence donor molecule complex or thequantum dot complex includes a third agent that has an affinity for thesecond target so that the two complexes are attracted to one another.

The interaction causes the two complexes to come in substantially closeproximity (e.g., 50 to 100 Angstroms), which would allow non-radiativeenergy transfer from the bioluminescence donor molecule to the quantumdot in the presence of the bioluminescence initiating molecule orcompound. The term “substantially close proximity” includes distancesthat allow for non-radiative energy transfer from the bioluminescencedonor molecule to the quantum dot in the presence of the bioluminescenceinitiating molecule or compound.

The reaction bioluminescence initiating molecule with thebioluminescence donor molecule causes the bioluminescence donor moleculeto emit bioluminescence energy. The non-radiative energy transfer fromthe bioluminescence donor molecule to the quantum dot can occur whenthere is an overlap (e.g., greater than 0.1%) between the emission andexcitation spectra of the donor and acceptor molecules, respectively.The energy is accepted by the quantum dot, and then the quantum dotemits fluorescent energy. The bioluminescence energy and/or thefluorescent energy can be detected and quantified in real time (e.g., invivo or in vitro) using an appropriate detection system. Additionaldetails are described in Example 4.

In an illustrative embodiment, the detection system used to measure thesignal from the self-illuminating quantum dot conjugate includes, but isnot limited to, a light tight module and an imaging device disposed inthe light tight module. The imaging device can include, but is notlimited to, a CCD camera and a cooled CCD camera. It should be notedthat other detection systems can be used to detect the bioluminescenceenergy and/or the fluorescent energy, such as, but not limited to, afluorometer, a luminometer, a multiple well microplate reader, and thelike.

In an embodiment, the self-illuminating quantum dot conjugates can bedetected in a system (e.g., a bioluminescence resonance energy transfer(BRET) system) using a detection system having a cooled charge-coupleddevice (CCD) camera, for example, capable of imaging low quantum yieldof visible light ranges from about 300 to 900 nm wavelength emitted fromsuperficial and deep tissue structures of small living subjects.

Self-Illuminating Quantum Dot Conjugates

As indicated above, the self-illuminating quantum dot conjugate caninclude, but is not limited to, a bioluminescence donor molecule and aquantum dot. In an embodiment, the bioluminescence donor molecule isbound (e.g., associated directly or indirectly) with the quantum dotprior to introduction to a system or host, while in another embodimentthe bioluminescence donor molecule and the quantum dot are not boundprior to introduction to a system or host. The term “bound” can includeways in which the bioluminescence donor molecule and the quantum dotinteract with one another to form the self-illuminating quantum dotconjugate. In general, the bioluminescence donor molecule and thequantum dot can be bound to one another by a physical, biological,biochemical, and/or chemical association directly or indirectly by asuitable means. The term “bound” can include, but is not limited to,chemically bonded (e.g., covalently or ionically), biologically bonded,biochemically bonded, and/or otherwise associated with the quantum dot.In an embodiment, bound can include, but is not limited to, a covalentbond, a non-covalent bond, an ionic bond, a chelated bond, as well asbeing bound through interactions such as, but not limited to,hydrophobic interactions, hydrophilic interactions, charge-chargeinteractions, π-stacking interactions, combinations thereof, and likeinteractions. In an embodiment, the quantum dot has amine groupsdisposed on the surface of the quantum dot, and the bioluminescencedonor molecule can conjugate with an amine group. The surface of thequantum dot can be coated with other compounds that have one or morefunctional groups that can conjugate with the bioluminescence donormolecule.

In general, a plurality of bioluminescence donor molecules is bound tothe quantum dot. The number of bioluminescence donor molecules perquantum dot can be controlled, at least in part, by controlling theconjugation conditions, the surface of the quantum dot, the type ofbioluminescence donor molecule, and the like. The number ofbioluminescence donor molecules per quantum dot may be about 1 to 100, 1to 75, 1 to 50, 1 to 30, 1 to 20, and 1 to 10. In an embodiment, themore bioluminescence donor molecules per quantum dot, the higher theemission intensity. Therefore, the number of bioluminescence donormolecules per quantum dot can be used to control the intensity of thequantum dot emission. Additional details about the bioluminescence donormolecule and the quantum dot are described below.

In an embodiment, the self-illuminating quantum dot conjugate or thebioluminescence donor molecule (or complex) and the quantum dot (orcomplex) can also include one or more types of agents bound (e.g.,associated directly or indirectly) to the bioluminescence donor moleculeand/or the quantum dot. The self-illuminating quantum dot conjugate orthe bioluminescence donor molecule (or complex) and the quantum dot (orcomplex) can include one or more agents that can be used to enhance theinteraction of the self-illuminating quantum dot conjugate with the hostor subject. The agent can have an affinity for a target such as, but notlimited to, a compound, a polypeptide, a polynucleotide, an antibody, anantigen, a hapten, a cell type, a tissue type, and the like. In anembodiment, the agent may be an antigen specific for an antibody thatcorresponds to a certain disease or condition. In another embodiment,the agent may be a first protein specific for another protein. Inanother embodiment, the agent may be a polynucleotide sequence specificfor a complementary polynucleotide sequence. In another embodiment, theagent can undergo a chemical, biological, and/or physical change, wherethe changed agent can have an affinity for another agent or target.

The agent can include, but is not limited to, polypeptides (e.g.,protein such as, but not limited to, an antibody (monoclonal orpolyclonal)), nucleic acids (both monomeric and oligomeric),polysaccharides, sugars, fatty acids, steroids, purines, pyrimidines,drugs (e.g., small compound drugs), ligands, or combinations thereof. Inan embodiment, the agent has an affinity for functional groups,compounds, cells, tissue, and the like, associated with a disease orcondition. The agent can have an affinity for one or more targets.

In another embodiment, the agent can make the self-illuminating quantumdot conjugate or the bioluminescence donor molecule (or complex) and thequantum dot (or complex) bio-compatible. In other words, theself-illuminating quantum dot conjugate can include a bio-compatibilitycompound. The bio-compatibility compound can include compounds such as,but not limited to, polyethylene glycol; polypropylene glycol 500,dextran, and derivatives thereof. The bio-compatibility compound can beattached directly or indirectly with the quantum dot and/or an agentbound to the quantum dot.

Thus, the agent can be selected so that the self-illuminating quantumdot conjugate can be used to image and/or diagnose the presence orabsence of the compounds, polypeptides, polynucleotides, antibodies,antigens, haptens, cell types, tissue types, and the like, associatedwith a disease or condition, or related biological activities.

In addition, the agent can also include, but is not limited to, a drug,a therapeutic agent, radiological agent, a small molecule drug, andcombinations thereof, that can be used to treat the target moleculeand/or the associated disease and condition of interest. The drug,therapeutic agent, and radiological agent can be selected based on theintended treatment as well as the condition and/or disease to betreated. In an embodiment, the self-illuminating quantum dot conjugatecan include two or more agents used to treat a condition and/or disease.

In an embodiment, the self-illuminating quantum dot conjugate or thebioluminescence donor molecule (or complex) and the quantum dot (orcomplex) can include at least two different types of agents, one being atargeting agent that targets certain cells or compounds associated witha condition and/or disease, while the second agent is a drug used totreat the disease. In this manner, the self-illuminating quantum dotconjugate acts as a detection component, a delivery component to thecells of interest, and a delivery component for the treatment agent. Thedetection of the self-illuminating quantum dot conjugate can be used toensure the delivery of the drug to its intended destination as well asthe quantity of self-illuminating quantum dot conjugates delivered tothe destination.

Quantum Dot

As indicated above, the self-illuminating quantum dot conjugate caninclude quantum dots such as, but not limited to, luminescentsemiconductor quantum dots. In general, quantum dots include a core anda cap, however, uncapped quantum dots can be used as well. The “core” isa nanometer-sized semiconductor. While any core of the IIA-VIA, IIIA-VA,or IVA-IVA, IVA-VIA semiconductors can be used in the context of thepresent disclosure, the core is preferably, upon combination with a cap,a result in a luminescent quantum dot. A IIA-VIA semiconductor is acompound that contains at least one element from Group IIA and at leastone element from Group VIA of the periodic table, and so on. Forexample, the core can be Au, CdS, CdSe, CdTe, ZnSe, ZnS, PbS, PbSe, oran alloy. It should also be noted that a quantum dot composite includinga quantum dot can be used as well (e.g., a hybrid of magneticnanoparticle with quantum dots, a carbon nanotube hybrid with quantumdots, and the like).

The core can include two or more elements. In one embodiment, the coreis a IIA-VIA, IIIA-VA, or IVA-IVA semiconductor that ranges in size fromabout 1 nanometer (nm) to 40 nm, about 1 nm to 30, about 1 nm to 20 nm,and about 1 nm to 10 nm. In another embodiment, the core is morepreferably a IIA-VIA semiconductor and ranges in size from about 2 nm to10 nm.

The “cap” is a semiconductor that differs from the semiconductor of thecore and binds to the core, thereby forming a surface layer on the core.The cap can be such that, upon combination with a given semiconductorcore, a luminescent quantum dot results. The cap should passivate thecore by having a higher band gap than the core. In one embodiment, thecap is a IIA-VIA semiconductor of high band gap. Combinations of thecore and cap can include, but are not limited to the following: the capis ZnS when the core is CdSe or CdS, and the cap is CdS when the core isCdSe. Other exemplary quantum dots include, but are not limited to, CdS,ZnSe, CdSe, CdTe, CdSe_(x)Te_(1-x), InAs, InP, PbTe, PbSe, PbS, HgS,HgSe, HgTe, CdHgTe, and GaAs. The cap is about 0.1 to 10 nm, about 0.1to 5 nm, and about 0.1 to 2 nm.

The wavelength emitted (i.e., color) by the quantum dots can be selectedaccording to the physical properties of the quantum dots, such as thesize and the material of the nanocrystal. Quantum dots are known to emitlight from about 300 nm to 2000 nm (e.g., UV, near IR, and IR). Thecolors of the quantum dots include, but are not limited to, red, blue,green, and combinations thereof. The color or the fluorescence emissionwavelength can be tuned continuously. The wavelength band of lightemitted by the quantum dot is determined by either the size of the coreor the size of the core and cap, depending on the materials that make upthe core and cap. The emission wavelength band can be tuned by varyingthe composition and the size of the QD and/or adding one or more capsaround the core in the form of concentric shells.

The intensity of the color of the quantum dots can be controlled. Foreach color, the use of 10 intensity levels (0, 1, 2, . . . 9) gives 9unique codes, because level “0” cannot be differentiated from thebackground. The number of codes increases exponentially for eachintensity and each color used. For example, a three color and 10intensity scheme yields 999 codes, while a six color and 10 intensityscheme has a theoretical coding capacity of about 1 million.

In general, it is more advantageous to use more colors, rather than moreintensity levels, in order to increase the number of usable codes. Thenumber of intensities is preferably from 0 to 20, more preferably about1 to 10. The number of colors is preferably about 1 to 10 (e.g., 2-8),and more preferably, about 3 to 7. By the term “multicolor quantum dot,”it is meant that more than one color of luminescent quantum dots isassociated with the same agent. For example two self-illuminatingquantum dot conjugates with different colored quantum dots are bound tothe same agent, so that both emit radiation when in contact with theparticular agent.

Quantum dots and the synthesis of quantum dots is well known and isdescribed in U.S. Pat. Nos. 5,906,670; 5,888,885; 5,229,320; 5,482,890;6,468,808; 6,306,736; 6,225,198; 6,906,339; 6,905,766; 6,846,475;6,743,400; 6,623,559; 6,528,165; 6,967,112; 6,794,265; 6,730,531;6,633,370; 5,989,947; 5,532,184; 5,202,290; and 5,170,226, (all of whichare incorporated herein by reference) and in many research articles. Thewavelengths emitted by quantum dots and other physical and chemicalcharacteristics have been described in U.S. Pat. No. 6,468,808 and thelike, and will not be described in any further detail. In addition,methods of preparation of quantum dots are described in U.S. Pat. No.6,468,808 and the like, and will not be described any further detail.

Bioluminescence Donor Molecule

The bioluminescence donor molecule can include, but is not limited to,luciferases, Renilla Luciferase, firefly Luciferase, aquorin, clickbeetle Luciferase, Gaussia Luciferase, horse radish peroxidase, andother bioluminescence donor molecules than can work with quantum dots,and combinations thereof. In addition, the bioluminescence donormolecule can include molecules as described in PCTUS06/34601 (entitled“Luciferases And Methods For Making And Using The Same”, filed on Sep.6, 2006), which is incorporated herein by reference in its entirety.

In an embodiment, the bioluminescence donor molecule can include, but isnot limited to, a Renilla Luciferase protein (as described herein and inthe example) (Rluc, SEQ ID NO:1), a mutated Renilla Luciferase protein(as described herein and in the example) (Rluc8, SEQ ID NO:2),conservatively modified variants of each, and combinations thereof. Themutated Renilla Luciferase protein can include, but is not limited to, 8mutations in the sequence, and these include A55T, C124A, S130A, K136R,A143M, M185V, M253L, and S287L (e.g., as described herein and in theexample). In addition, the mutated Renilla Luciferase protein caninclude conservatively modified variants of one or more of thesemutations as long as the conservatively modified variant retains thecharacteristics of the mutated Renilla Luciferase protein.

In an embodiment, when the bioluminescence donor molecule is a mutatedRenilla Luciferase protein, the bioluminescence sensitivity increase ofabout 20 to 60 fold or more and about 40 fold can be realized. Also inembodiments using the mutated Renilla Luciferase protein, the mutatedRenilla Luciferase protein is more stable relative to other proteins.

In general, the mutated Renilla Luciferase protein is very stable. Ithas been shown that a C124A mutation increases the stability of RLuc. Inorder to further enhance the stability of RLuc, a number of mutationscan be included in addition to the C124A mutation. The combination of 8favorable mutations including C124A generated a mutant Renillaluciferase (RLuc8) that exhibited a greater than 150-fold stabilityimprovement in murine serum when compared to native Rluc (<1 hrversus >100 hr) and increased the sensitivity of the system by about 20to 60 fold and about 40 fold relative to native Renilla Luciferase. Inaddition to being more stable, RLuc8 also exhibited at least a 4-foldimprovement in light output, along with red shift of about 5 nm to itsemission spectrum with respect to the native Rluc. The RenillaLuciferase protein and the mutated Renilla Luciferase protein aredescribed in more detail in the Examples and in Nature Biotechnology2006 (See, So M-K, Xu C, Loening A M, Gambhir S S, Rao J.Self-illuminating quantum dot conjugates for in vivo imaging. NatureBiotechnology 2006; 24: 339-343 and PCT Application filed on Mar. 10,2006 having PCT/US06/08632 and entitled “BIOLUMINESCENCE RESONANCEENERGY TRANSFER (BRET) SYSTEMS AND METHODS OF USE THEREOF”, and PCTApplication filed on Sep. 6, 2006 having PCT/US2006/034601 and entitled“LUCIFERASES AND METHODS FOR MAKING AND USING THE SAME”, each of whichare incorporated herein by reference).

The agent and/or bioluminescence donor molecule can be linked to thequantum dot using any stable physical and/or chemical association to thequantum dot directly or indirectly. In general, the agent and/orbioluminescence donor molecule can be linked to the quantum dot using,but not limited to, a covalent link, a non-covalent link, an ionic link,a chelated link, as well as being linked to the quantum dot throughinteractions such as, but not limited to, hydrophobic interactions,hydrophilic interactions, charge-charge interactions, π-stackinginteractions, combinations thereof, and like interactions. Inembodiments a linker can be used to link the one or more of thecomponents (e.g., the quantum dot, the bioluminescence donor moleculesagent an the like).

The linker can be a compound that includes one or more functional groupsto attach one or more of the quantum dot, the agent, bioluminescencedonor molecule, and/or other components of the self-illuminating quantumdot conjugate. The linker can include functional groups such as, but notlimited to, amines, carboxylic acids, hydroxyls, thios, and combinationsthereof. The linker can include compounds such as, but not limited to,DTPA, EDTA, DOPA, EGTA, NTA, and combinations thereof.

Bioluminescence Initiating Compound

As mentioned above, the self-illuminating quantum dot conjugate is usedin conjunction with a bioluminescence initiating compound to produce aradiation emission that is absorbed by the quantum dot. Thebioluminescence initiating compound can include, but is not limited to,coelenterazine, analogs, and functional derivatives thereof, andD-luciferin analogs, and functional derivatives thereof. Derivatives ofcoelenterazine include, but are not limited to, coelenterazine 400a,coelenterazine cp, coelenterazine f, coelenterazine fcp, coelenterazineh, coelenterazine hcp, coelenterazine ip, coelenterazine n,coelenterazine 0, coelenterazine c, coelenterazine c, coelenterazine i,coelenterazine icp, coelenterazine 2-methyl, and deep bluecoelenterazine (DBC) (described in more detail in U.S. Pat. Nos.6,020,192; 5,968,750 and 5,874,304, which are incorporated herein byreference). In an embodiment, the bioluminescence initiating compoundcan be D-luciferine when the bioluminescence compound is fireflyluciferase.

In general, coelenterazines are known to luminesce when acted upon by awide variety of bioluminescent proteins, specifically luciferases.Coelenterazines disclosed in U.S. patent application Ser. No.10/053,482, filed Nov. 2, 2001 (which is hereby incorporated byreference in its entirety), could be used as well. Coelenterazines areavailable from Promega Corporation, Madison, Wis. and from MolecularProbes, Inc., Eugene, Oreg. Coelenterazines may also be synthesized asdescribed for example in Shimomura et al., Biochem. J. 261: 913-20,1989; Inouye et al., Biochem. Biophys. Res. Comm. 233: 349-53, 1997; andTeranishi et al., Anal. Biochem. 249: 37-43, 1997, which areincorporated herein by reference.

Methods of Use

As mentioned above, the present disclosure relates generally to methodsfor studying (e.g., detecting, localizing, or quantifying) cellularevents, in vivo cell trafficking, stem cell studies, tumor imaging,biomolecule array systems, biosensing, biolabeling, gene expressionstudies, protein studies, medical diagnostics, diagnostic libraries,microfluidic systems, and delivery vehicles. The present disclosure alsorelates to methods for multiplex imaging of multiple eventssubstantially simultaneously inside a subject (e.g., a host living cell,tissue, or organ, or a host living organism) using one or moreself-illuminating quantum dot conjugates without the use of an externalexcitation source for the quantum dot. It should be noted that thebioluminescence donor molecule (or complex) and the quantum dot (orcomplex) can be used in methods using the self-illuminating quantum dotconjugates.

In short, the self-illuminating quantum dot conjugates are introduced tothe subject using known techniques. The self-illuminating quantum dotconjugates can also be labeled with one or more types of agents for theparticular study (e.g., agents directed to cancer imaging and/ortreatment), as mentioned above. In addition, a single agent can beassociated with two or more types of self-illuminating quantum dotconjugates, where the self-illuminating quantum dot conjugates includedifferent quantum dots.

At an appropriate time (e.g., before, after, or at the same time as theself-illuminating quantum dot conjugate), the bioluminescence initiatingcompound is introduced to the host living cell, tissue, or organ, or ahost living organism. In an embodiment, the appropriate time may includea time frame to allow unassociated self-illuminating quantum dotconjugates to be sufficiently cleared from the appropriate area, region,or tissue of interest. The bioluminescence initiating compound can reactwith the bioluminescence donor molecule. The reaction causes thebioluminescence donor molecule to emit bioluminescence energy. Theenergy transfer from the bioluminescence donor molecule to the quantumdot can occur when there is an overlap between the emission andexcitation spectra of the donor and acceptor molecules, respectively.The energy is accepted by the quantum dot, and then the quantum dotemits fluorescent energy. The bioluminescence energy and/or thefluorescent energy can be detected and quantified in real time using adetection system. The measured signal is or can be correlated to thefeature being studied. In an embodiment, the detection of thebioluminescence energy and/or the fluorescent energy can be conductedafter a sufficient time frame to allow unassociated self-illuminatingquantum dot conjugates to be sufficiently cleared from the appropriatearea, region, or tissue of interest.

In an embodiment, the self-illuminating quantum dot conjugates can beused to study, image, diagnose the presence of, and/or treat cancerouscells, precancerous cells, cancer, or tumors. It should be noted thatself-illuminating quantum dot conjugate can include agents specific forother diseases or conditions so that other diseases or conditions can beimaged, diagnosed, and/or treated using embodiments of the presentdisclosure. In an embodiment, other diseases and/or conditions can bestudied, imaged, diagnosed, and/or treated in a manner consistent withthe discussion below as it relates to cancerous cells, precancerouscells, cancer, and/or tumors.

In an embodiment, the self-illuminating quantum dot conjugates can beused to study, image, diagnose the presence of, and/or treat cancerouscells, precancerous cells, cancer, or tumors. The self-illuminatingquantum dot conjugates include an agent that can be degraded in thepresence of one or more components present with cancerous cells,precancerous cells, cancer, or tumors. When the agent degrades theself-illuminating quantum dot conjugate, the quantum dot does not emit afluorescent energy. In other words, the self-illuminating quantum dotconjugate initially emits a fluorescent energy from the quantum dot, butthe emission decays as the component degrades the polypeptide, whichcauses the self-illuminating quantum dot conjugate to degrade intomultiple components (e.g., quantum dot and bioluminescence donormolecule). It should be noted that other diseases and/or conditionscould be studied, imaged, diagnosed, and/or treated in a mannerconsistent with the discussion above.

For example, a polypeptide sequence (or other linker) can be placedbetween the quantum dot and the bioluminescence donor molecule. Thepolypeptide degrades in the presence of a component present withcancerous cells, precancerous cells, cancer, or tumors. Therefore, theself-illuminating quantum dot conjugate initially emits a fluorescentenergy from the quantum dot, but the emission decays as the componentdegrades the polypeptide, which causes the self-illuminating quantum dotconjugate to degrade into multiple components. Additional details arediscussed in Example 3.

In an embodiment, the self-illuminating quantum dot conjugate caninclude one or more agents that has an affinity for cancerous cells,precancerous cells, cancer, or tumors, so that upon introduction to thesubject, the self-illuminating quantum dot conjugates coordinate withthe cancerous cells, precancerous cells, cancer, or tumors. Abioluminescence initiating compound can be introduced to the subject andreact with the bioluminescence donor molecule to produce an emissionfrom the quantum dot. Thus, upon measuring the emitted energy from thequantum dot and/or the bioluminescence donor molecule, one can imageand/or diagnose the presence of the cancerous cells, precancerous cells,cancer, or tumors.

In another embodiment, the self-illuminating quantum dot conjugateincludes one or more agents to treat the cancerous cells, precancerouscells, cancer, or tumors. A bioluminescence initiating compound can beintroduced to the subject and react with the bioluminescence donormolecule to produce an emission from the quantum dot. Thus, uponmeasuring the emitted energy from the quantum dot and/or thebioluminescence donor molecule, one can determine if theself-illuminating quantum dot conjugate has coordinated with thecancerous cells, precancerous cells, cancer, or tumors. Embodiments ofthe self-illuminating quantum dot conjugate can aid in visualizing theresponse of the cancerous cells, precancerous cells, cancer, or tumorsto the agent.

In another embodiment, the self-illuminating quantum dot conjugate caninclude one or more coordinating agents that has an affinity forcancerous cells, precancerous cells, cancer, or tumors as well as one ormore treating agents to treat the cancerous cells, precancerous cells,cancer, or tumors. A bioluminescence initiating compound can beintroduced to the subject and react with the bioluminescence donormolecule to produce an emission from the quantum dot. Thus, uponmeasuring the emitted energy from the quantum dot and/or thebioluminescence donor molecule, one can image the cancerous cells,precancerous cells, cancer, or tumors as well as determine what portionsof the cancerous cells, precancerous cells, cancer, or tumors are beingtreated by the treatment agent.

In general, the self-illuminating quantum dot conjugates can be used ina screening tool to select agents for imaging, diagnosing, and/ortreating a disease or condition. In an embodiment, the self-illuminatingquantum dot conjugates can be used in a screening tool to select agentsfor imaging, diagnosing, and/or treating cancerous cells, precancerouscells, cancer, or tumors. The self-illuminating quantum dot conjugatescan be imaged and it can be determined if each agent can be used toimage, diagnose, and/or treat cancerous cells, precancerous cells,cancer, or tumors.

Kits

This disclosure encompasses kits that include, but are not limited to,self-illuminating quantum dot conjugates (e.g., with one or more agentsas described above), a bioluminescence initiating compound, anddirections (written instructions for their use). In another embodiment,the kits include, but are not limited to, bioluminescent donor compounds(complex), quantum dot conjugates (complex) (e.g., with one or moreagents as described above), a bioluminescence initiating compound, anddirections (written instructions for their use). The components listedabove can be tailored to the particular cellular event being studiedand/or treated (e.g., cancer, cancerous, or precancerous cells). The kitcan further include appropriate buffers and reagents known in the artfor administering various combinations of the components listed above tothe host cell or host organism.

EXAMPLES

Now having described the embodiments of the self-illuminating quantumdot conjugates, systems, and methods of use, in general, examples 1-4describe some additional embodiments of the self-illuminating quantumdot conjugates, systems, and methods of use. While embodiments ofself-illuminating quantum dot conjugates, systems, and methods of useare described in connection with examples 1-4 and the corresponding textand figures, there is no intent to limit embodiments of theself-illuminating quantum dot conjugates, systems, and methods of use tothis description. On the contrary, the intent is to cover allalternatives, modifications, and equivalents included within the spiritand scope of embodiments of the present disclosure.

Example 1 Discussion:

This example provides an embodiment of a conjugation method thatutilizes a genetically engineered hydrolase to covalently immobilize abioluminescent protein at the quantum dot surface. The immobilizedbioluminescent protein can efficiently produce chemical energy to excitequantum dots via resonance energy transfer.

An embodiment of a method employs a commercially available, engineeredhaloalkane dehalogenase—the HaloTag protein (HTP) (See, TechnicalManual, Promega, “HaloTag™ Interchangeable Labeling Technology”;http://www.promega.com, 2006, which is incorporated herein byreference). The native enzyme is a monomeric protein (MW ˜33 KDa) thatcleaves carbon halogen bonds in aliphatic halogenated compounds. Uponthe nucleophilic attack to Asp106 in the enzyme by the chloroalkane, anester bond is formed between the HaloTag ligand and the protein (FIG. 1,Scheme 1). HTP contains a critical mutation in the catalytic triad(His272 to Phe) so that the formed ester bond between HTP and HaloTagligand cannot be further hydrolyzed (FIG. 1, Scheme 1). HaloTag ligandslabeled with small organic dyes such as coumarin and fluorescein havebeen developed for in vivo labeling of target proteins. This technologyis applied for the specific conjugation of proteins to quantum dots.

To take advantage of this specific protein-ligand interaction, quantumdots can be functionalized with HaloTag ligands. A protein target can inturn be genetically fused to HTP at either its N- or C-terminus. Theresulting fusion protein can then be conjugated to quantum dots throughthe reaction between HaloTag ligands and HTP (FIG. 1, Scheme 1).

To demonstrate the utility of this method for quantum dot conjugation, abioluminescent protein, Renilla luciferase, was selected as the target.It was demonstrated that when Renilla luciferase is conjugated toquantum dots, bioluminescence resonance energy transfer (BRET) can takeplace (See, M.-K. So, C. Xu, A. M. Loening, S. S. Gambhir, J. Rao,Nature Biotechnol. 2006, 24, 339-343, which is incorporated herein byreference). Such quantum dot conjugates can emit light without lightexcitation, and offer greatly improved sensitivity for in vivo imaging.With Renilla luciferase as the target protein for the conjugation, theconjugation reaction can be conveniently evaluated from the BRETemission of the quantum dots—a measure of both the conjugation chemistryand the function of the conjugated luciferase.

A stabilized mutant of Renilla luciferase (Luc8) was genetically fusedto the N-terminus of the HTP and expressed to obtain the fusion proteinHTP-Luc8. The C-terminus of HTP-Luc8 contained a 6xHis tag to facilitateits purification. Gel electrophoresis analysis indicated that themolecular weight of the fusion protein was consistent with the expectedvalue, ˜70 kDa (FIG. 3 a). The bioluminescence activity of the fusionprotein was estimated to be 1.2×10²³ photons/s/mole, ˜86% of Luc8 (FIG.3 b).

In order to minimise potential steric hindrance between the quantum dotsand HaloTag proteins during conjugation, a HaloTag ligand was designedcontaining an amino ethylene glycol group that would help present theligand away from the quantum dot surface (FIG. 1, Scheme 1). The HaloTagligand 1 was prepared from 6-chloro-1-iodohexane and2-(2-aminoethoxy)ethanol by following the synthetic route outlined inFIG. 2, Scheme 2, and was immobilized through its amino group to thecarboxylate-presenting quantum dots (QD@COOH). The resulting quantumdots coated with the HaloTag ligand 1 (QD@1) showed good solubility inneutral pH buffer. The conjugation of the fusion protein HTP-Luc8 toQD@1 was carried out by a simple mixing of both at 37° C., resulting inan irreversible covalent bond formation between ligand 1 on quantum dotsand HTP-Luc8.

Since successful immobilization of HTP-Luc8 to quantum dots should allowBRET to occur, the BRET emission was measured from the quantum dotsfollowing the conjugation reaction. Addition of coelenterazine, thesubstrate for Renilla luciferase, to the purified conjugateQD@1-HTP-Luc8 resulted in a dual-peak bioluminescence emission spectrum.In addition to the Luc8 peak at 480 nm, there was an emission maximum at655 nm that overlapped well with the fluorescence emission of thequantum dot conjugates excited at 480 nm (FIG. 4).

To evaluate whether the observed BRET emission was due to specificconjugation between the quantum dots and fusion proteins, the dependenceof the BRET emission on the HaloTag ligand 1 used in the conjugation wasexamined. QD@COOH was first functionalized with various concentrationsof 1. These modified quantum dots were subsequently conjugated with 20equivalents of HTP-Luc8. FIGS. 5 and 6 show that with increasing amountsof ligand 1 used in the conjugation, the bioluminescence emissions fromboth the immobilized HTP-Luc8 and the quantum dots via BRET increased.When quantum dots without HaloTag ligand 1 attached were similarly mixedwith the fusion protein, there were only a small emission from HTP-Luc8at 480 nm and a small BRET emission from the quantum dots. The smallBRET emission probably arises from an electrostatic interaction betweenthe 6xHis tag on HTP-Luc8 and the negative carboxylate groups on thequantum dots. These results confirm that the BRET emission reflectsspecific conjugation occurring between the quantum dots and the fusionprotein HTP-Luc8, and that the conjugation does not affect the enzymaticactivity of the fusion protein HTP-Luc8.

The efficiency of the resonance energy transfer process can bequantitatively estimated from the BRET ratio. The BRET ratio is definedby the acceptor emission relative to the donor emission (See, M.-K. So,C. Xu, A. M. Loening, S. S. Gambhir, J. Rao, Nature Biotechnol. 2006,24, 339-343, K. D. G. Pfleger, K. A. Eidne, Nat. Methods 2006, 3,165-174, which are incorporated herein by refrence). In the quantum dotand HTP-Luc8 conjugate, the donor is Luc8 and the acceptor is quantumdots. The BRET ratio was calculated by dividing the total emission fromthe quantum dots by the total emission from HTP-Luc8, shown in FIG. 5 b.With the increase in the number of HaloTag ligand 1 and, in turn, theincrease in immobilized fusion protein, the BRET ratio decreasedgradually from 0.6 to 0.4. In principle, the BRET ratio should notdepend on the number of immobilized proteins if the BRET distanceremains unchanged. This small decrease in the BRET ratio may be due to ashift in the orientation of the conjugated fusion proteins on thequantum dot surface (A larger number of immobilized proteins would leadto denser packing at the surface, resulting in the Luc8 domain of thefusion proteins being pushed further away from the quantum dot surfaceand consequently a larger average BRET distance).

Finally, the dependence of the conjugation reaction on the amount offusion protein present was examined. Quantum dots were reacted with 1000equivalents of HaloTag ligand 1, and then reacted with increasingconcentrations of HTP-Luc8. As expected, the resulting conjugates showedincreasing bioluminescence emissions both from HTP-Luc8 and from thequantum dots (FIG. 7). As a control, Luc8 (without HTP fusion) wasincubated with the QD@1. The control reaction showed no bioluminescenceemission, indicating no immobilization of Luc8 on the quantum dots andfurther confirming that the conjugation between quantum dots andHTP-Luc8 was specific.

In summary, this example describes embodiments based on the specificinteraction between the HaloTag protein and its ligand, to functionalizequantum dots for biological imaging. Using this method, a bioluminescentprotein was conjugated to quantum dots and produced self-illuminatingquantum dot conjugates.

Materials and Methods:

Chemicals for HaloTag ligand synthesis were from Sigma-Aldrich. Thecoupling reagent 1-ethyl-3-(3-dimethylaminopropyl)carbodiimidehydrochloride (EDC) was from Fluka. Quantum dots were purchased fromInvitrogen, and have CdSe/ZnS core-shell structures with a quantum yield(determined in 50 mM pH 9borate buffer) of 83%. Coelenterazine was fromProlume. The plasmid pHT2 (HaloTag) was from Promega. NanoSep 100Kfilters for quantum dot purification were from Pall, Life Science.

Synthesis of 1: the compound was synthesized from 6-chloro-1-iodohexaneand 2-(2-aminoethoxy)ethanol according to FIG. 2, Scheme 2. NMR: (400MHz, CDCl₃) δ 3.92 (s, 2H), 3.70-3.20 (m, 18H), 2.09 (m, 2H), 2.64 (m,2H), 2.50 (m, 2H), 1.40-1.20 (s, 4H). LC-MS: m/z 369.2 [M+1]⁺; calc. M⁺:368.2.

Conjugation of 1 to quantum dots: Quantum dots, HaloTag ligand 1, andEDC (400 equiv.) were mixed together in borate buffer (10 mM, pH 7.4)and incubated at room temperature for 1 hour. QD@1 was separated fromfree HaloTag ligand and excess EDC by filtration through a 100K NanoSepfilter. The quantum dot conjugates were washed 3 times with pH 8.5borate buffer for 1 hr before recovered with pH 7.4 borate buffer. Theconcentration of QD@1 was determined from the fluorescence intensity.

Preparation and purification of HTP-Luc8: the plasmid pBAD-Luc8-HaloTagencoded for the fusion protein was constructed from plasmid pBAD-RLuc8and plasmid pHT2 by PCR and ligation. E. coli LMG194 cells transformedwith this plasmid were induced with 0.2% arabinose and grown at 32° C.to an OD₆₀₀ of 0.7. Cells were lysed by thawing in wash buffer (WB: 300mM NaCl, 20 mM HEPES, 20 mM imidazole, pH 8) containing 1 mg/mllysozyme, 10 μg/ml RNAse A, and 5 μg/ml DNAse I. Lysates were clarifiedby centrifugation and allowed to bind to nickel affinity resin (Ni-NTASuperflow, Qiagen) for 1 h at 4° C. with gentle mixing. After washingwith WB, protein was eluted with elution buffer (300 mM NaCl, 20 mMHEPES, 250 mM imidazole, pH 8), further purified by anion exchangechromatography (Source 15Q resin, GE/Amersham), and followed by gelfiltration chromatography with borate buffer.

Conjugation of QD@1 with HTP-Luc8: Typically 5 pmol of QD@1 wasincubated with 20 equiv. of HTP-Luc8 in borate buffer (pH 7.4, 10 mM) at37° C. for 30 m. Free HTP-Luc8 was removed from the incubation mixtureby filtration through a 100K NanoSep filter at 4° C. The filteredconjugates were washed efficiently with pH 7.4 borate buffer at 4° C.The final quantum dot conjugates were recovered with ice cold pH 7.4borate buffer.

Fluorescence and bioluminescence spectra were collected with a FluoroMax-3 (Jobin Yvon Inc.). Bioluminescence spectra were acquired withexcitation light blocked.

Example 2 Introduction:

Fluorescent semiconductor quantum dots (QDs) have held excitingpotential for molecular imaging in living biological samples since theirinitial development; however, all existing QDs require excitation fromexternal illumination sources in order to fluoresce, which limits theirapplication in imaging of living opaque subjects due to the resultantstrong autofluorecence background and a paucity of excitation light atnon-superficial locations. This example presents a new type of QDconjugates that can luminesce not by external illumination but viabioluminescence resonance energy transfer (BRET). These bioluminescentQD conjugates were prepared by coupling carboxylate-presenting QDs to amutant of the bioluminescent protein Renilla luciferase, and were shownto emit long-wavelength (from red to near-infrared) bioluminescentlight. This example demonstrates that bioluminescent QD conjugates canbe imaged in living cells and in living animals, even in deep tissues,and are suitable for multiplex in vivo bioluminescence imaging.Availability of these bioluminescent QD conjugates will enable many newpossibilities for imaging biological events in living subjects.

Much of the excitement towards QDs arises from their unique opticalproperties as fluorescence imaging probes in comparison to traditionalorganic fluorophores, such as high quantum yield, high molar extinctioncoefficients, narrow emission spectra, size-dependent tunable emission,and high photostability, all of which make QDs appealing for in vivoimaging. QDs fabricated with various coating molecules andfunctionalized with biomolecules such as small peptides, proteins,antibodies, and nucleic acids, have been applied in a number of imagingstudies. All reported QDs, however, need excitation from externalillumination sources in order to fluoresce, which often presents aninherent challenge in imaging opaque subjects such as small livinganimals. In biological tissues, there are ubiquitous endogenouschromophores such as collagens, porphyrins, and flavins, which are alsoexcited and lead to significant background autofluorescence. Inaddition, short-wavelength excitation photons are largely absorbed intissues, therefore, little light reaches and excites QDs present atnon-superficial locations. To avoid these problems, ideal QDs would emitlight with no need for excitation from external illumination sources.Such QDs would be more applicable for molecular imaging in small livingsubjects.

Discussion:

This example describes a design for QD conjugates that can luminescewithout external illumination sources based on the principle ofbioluminescence resonance energy transfer (BRET). BRET is a naturallyoccurring phenomenon where a light emitting protein (the donor)non-radiatively transfers energy to a fluorescent protein (the acceptor)in close proximity. For example, in the sea pansy Renilla reniformis,the energy generated in the luciferase-catalyzed oxidation of thesubstrate coelenterazine is transferred to a green fluorescent protein(GFP) and emitted as green wavelength photons. Replacing GFP with a QD,the bioluminescence energy of the luciferase-catalyzed reaction could betransferred to the QD, resulting in light emission from the QD (FIG. 8a). A number of recent studies have demonstrated that fluorescenceresonance energy transfer (FRET) can take place between QDs and organicdyes, but it has not been documented whether bioluminescence energy canbe transferred to QDs. Furthermore, all reported QD FRET examples haveused QDs as the energy donor, and it has been argued that QDs cannot beFRET acceptors for organic fluorophores.

Luciferase-based in vivo bioluminescence imaging has become a popularand powerful imaging technique for the study of biology due to itsextremely high sensitivity. There are two commonly used luciferases:firefly luciferase that catalyzes the oxidation of D-luciferin in thepresence of oxygen, ATP, and Mg²⁺, with a maximal emission around 560nm, and Renilla luciferase that catalyzes the oxidation ofcoelenterazine, with a maximal emission around 480 nm. D-luciferin andcoelenterazine are administrated via intravenous or intraperitonealinjections at low doses that have not yet demonstrated any significantperturbation or toxicity to the subject. For the designing ofbioluminescent QD conjugates, Renilla luciferase is better suited as theBRET donor since QDs absorb blue light more efficiently than light atlonger wavelengths (FIG. 8 b). A mutant of Renilla luciferase(containing 8 mutations and thus designated as “Luc8”) with high serumstability and improved catalytic efficiency has been developed aspreviously mentioned above. Addition of the substrate, coelenterazine,to Luc8 led to the emission of blue light peaked at 480 nm (FIG. 8 b).Luc8 was conjugated to polymer-coated CdSe/ZnS core-shell QD655 (withfluorescence emission at 655 nm) through amide coupling of the aminogroups on Luc8 to carboxylates presented on the surface of the QDs. Gelelectrophoresis analysis indicated altered mobility for the QD655-Luc8conjugate compared to the unconjugated QD655, confirming successfulconjugation (FIG. 8 c). The hydrodynamic diameter of QD655-Luc8conjugates, measured by quasi-elastic light scattering, was increased byapproximately 2 nm in comparison to QD655. Each QD655-Luc8 conjugate wasestimated to contain on average six copies of Luc8.

The bioluminescence emission of the QD655-Luc8 conjugate was examinedupon the addition of coelenterazine (FIG. 8 d). In addition to thebioluminescence emission of Luc8 at 480 nm, a strong new emission peakat 655 nm was detected, which is consistent with BRET occurring in ourconjugate. The BRET ratio is determined by dividing the acceptoremission by the donor emission, and was 1.29 for our QD655-Luc8conjugate (corresponding to an efficiency of 56%). For one mole ofQD655-Luc8, the maximal blue photon emission (at 480 nm from Luc8) is3.0×10²² photons/s, and the maximal QD655 emission is 3.6×10²²photons/s. In contrast, one mole of Luc8 in the borate buffer produces1.5×10²² photons per second under saturating concentrations ofcoelenterazine.

The BRET ratio was dependent on the distance between Luc8 and QD655.When the mean distance between Luc8 and QD655 was increased byapproximately 2-3 nm, the BRET ratio dropped to ˜0.37 (FIG. 12). Whenthe ratio of QD655 to Luc8 in the coupling reaction was varied to makeconjugates with varying numbers of Luc8, the BRET ratio among theseconjugates was surprisingly similar, ranging from 1.10 to 1.46, althoughthe intensity of both Luc8 and QD emission varied significantly (FIG.13). In QD FRET examples where QDs serve as the donor, the FRETefficiency increased with increasing numbers of the FRET acceptor perQD. In contrast, the measured BRET efficiency in this QD-Luc8 conjugateis not the sum but the average of the resonance energy transferefficiency from each individual Luc8 to the QD.

To assess whether BRET emission can be detected in living subjects, theemission of QD655-Luc8 (5 pmol) in mouse serum and whole blood was firstexamined. While the Luc8 emission nearly disappeared in whole bloodbecause of absorption by hemoglobin, the BRET emission was not effected(FIG. 8 e). A solution of QD655-Luc8 (5 pmol) was subcutaneouslyinjected into the left shoulder of a nude mouse (injection site I inFIG. 9 a). As a comparison, in the same mouse, a solution of Luc8 (30pmol) was similarly injected into the right shoulder (II in FIG. 9 a).Coelenterazine (10 μg) was subsequently injected via tail-vein, and themouse was imaged sequentially: without any emission filter (so theemission from both Luc8 and QD655 was collected; FIG. 9 a) and with anemission filter (575-650 nm, to collect the QD655 emission; FIG. 9 b).Images collected without any emission filter showed strong emissionintensities from both injection sites (FIG. 9 a). The total photonfluxes from both sites were similar, indicating that the total activityof Luc8 was approximately the same at both sites. With the filter, therewas still a strong signal from site I (left shoulder, QD655-Luc8, FIG. 9b), which was 60% of the intensity collected without the filter.However, the signal from Luc8 (right shoulder, FIG. 9 b) was just 25% ofthat collected without the filter. When a narrow filter (650-660 nm) wasused for the collection of only the BRET emission, there was an evenlower amount of signal detected from site II (Luc8 injected in the rightshoulder) while site I (QD655-Luc8 injected in the left shoulder) stillemitted strongly (FIG. 14). These results indicate that BRET occursbetween Luc8 and QDs and is detectable in living subjects at superficialdepths.

The detection of the BRET emission of QD655-Luc8 was compared to theLuc8 emission in deeper tissues. A solution of QD655-Luc8 (5 pmol) wasinjected intramuscularly (at the depth of about 3 mm; injection III inFIG. 9 a). As a comparison, a solution of Luc8 (30 pmol) was similarlyinjected into the same nude mouse (injection IV in FIG. 9 a). Incontrast to the subcutaneous injections (injections I and II in FIG. 9a), even without any filter, the emission of intramuscularly injectedLuc8 was much weaker than QD655-Luc8 (IV vs III in FIG. 9 a): the totaldetected photons from site IV was only 26% of that from site III. Withthe filter (575-650 nm), there was little detectable signal from theinjected Luc8 but still a strong signal from the QD655-Luc8 conjugate(FIG. 9 b). The bioluminescence intensity of the injected QD655-Luc8imaged with the filter was 75% of the intensity without the filter. Theincreased ratio of detected QD655 emission versus Luc8 emission is dueto preferential absorption of the shorter wavelength light (Luc8emission) in tissues. Therefore, in deep tissues, the longer wavelengthBRET emission of QD655-Luc8 is more readily detected than the shortwavelength emission from Luc8.

The same mouse was examined with fluorescence spectral imaging for QDemission at sites where QD655-Luc8 was injected. A strong signal wasobserved from subcutaneously injected QD655-Luc8 (site I), butintramuscularly injected QD655-Luc8 (site III) emitted little signal(FIG. 9 c). This result demonstrates the advantage of bioluminescencedetection of signals from deep tissues with bioluminescent QDconjugates.

One long-sought feature for in vivo bioluminescence imaging is to have anumber of probes with distinct long-wavelength emissions to enablemultiple target imaging. Since QDs have similar absorption spectra andall absorb blue wavelength light efficiently, Luc8 can serve as the BRETdonor for other QDs than QD655 (FIG. 10 a). Conjugates QD705-Luc8,QD800-Luc8, and QD605-Luc8 were similarly prepared. FIG. 10 b displaysthe fluorescence emission spectrum of each QD conjugate, while FIG. 10 cshows the bioluminescence spectrum of each QD conjugate upon theaddition of coelenterazine. Clearly, BRET occurs in each conjugate. TheBRET ratio of each conjugate is estimated as 0.70 for QD605-Luc8, 1.20for QD655-Luc8, 2.30 for QD705-Luc8, and 1.32 for QD800-Luc8. This trendcorrelates well with the excitability of each QD (Example 2, Table 1).For example, QD705 and QD800 have the same extinction coefficient(1,700,000 M⁻¹cm⁻¹ at 550 nm), but the quantum yield of QD705 is 80% andonly 43% for QD800, hence the BRET ratio of QD800-Luc8 is just abouthalf of QD705-Luc8.

TABLE 1 The BRET ratio of QD-Luc8 conjugates. Quantum ExtinctionCoefficient QD-Luc8 Yield ^(a) (M⁻¹cm⁻¹) ^(a) BRET Ratio QD605 65%  650,000 (at 596-604 nm) 0.70 QD655 83%   800,000 (at 638 nm) 1.20-1.29QD705 80% 1,700,000 (at 550 nm) 2.30 QD800 43% 1,700,000 (at 550 nm)1.32 ^(a) Product specifications from Quantum Dot Corporation (Hayward,California).

The spectrally distinct emissions from the four QD conjugates makemultiplex bioluminescence imaging feasible. This possibility wasexamined by first imaging solutions containing QD605-Luc8, QD655-Luc8,QD705-Luc8, QD800-Luc8, and their mixtures in vitro (FIG. 10 d-e). Usingbioluminescence spectral imaging, which is analogous to fluorescencespectral imaging but without excitation light, the bioluminescenceemission from each conjugate could be selectively distinguished from theemissions of the other conjugates when it was either alone or mixed withthe other conjugates.

QD655-Luc8 (5 pmol), QD705-Luc8 (15 pmol), QD800-Luc8 (15 pmol), and amixture of all three conjugates were injected intramuscularly at fourdifferent sites on a nude mouse. After tail-vein injection ofcoelenterazine, the mouse was imaged for the bioluminescence emissionfrom the conjugates. The total emission (from both Luc8 and BRET) wascollected without any filter (FIG. 100, and the BRET emission of eachconjugate was collected with appropriate filters, for example, x-Cy5.5filter for QD705-Luc8, and ICG filter for QD800-Luc8 (FIG. 10 g-i).Similarly to the in vitro imaging data, all conjugates showed Luc8emission, and each BRET emission was readily distinguished withappropriate filters, although there was a small degree of signalcross-talking due to the overlapping of the emission spectra betweenQD655-Luc8 and QD705-Luc8, and between QD705-Luc8 and QD800-Luc8 (FIG.10 b). With optimized filters ideal for QDs, the small degree of signalcross-talking can be prevented.

Finally, the BRET conjugates were evaluated whether they could labelliving cells and monitor labeled cells in living animals. QD655-Luc8 byitself was able to enter living cells, but the uptake efficiency wasimproved when it was conjugated with a polycationic peptide such as anarginine 9-mer (QD655-Luc8-R9). The BRET ratio of QD655-Luc8-R9 wascomparable to that of QD655-Luc8, indicating little impact on BRET fromthe additional conjugation of the arginine 9-mer. Cells incubated withQD655-Luc8-R9 for one hour at 37° C. displayed bright QD655 signals whenobserved under a fluorescence microscope (FIG. 11 a). These cells werecollected for assaying the luciferase activity, and upon the addition ofcoelenterazine, bright luminescence light was detected both in theabsence and presence of the long wavelength filter (575-650 nm) (FIG. 11b). Without a filter, both the emissions from Luc8 and QD655 weredetected (right tube in FIG. 11 b); in the presence of the filter, thedetected signal should mostly result from the BRET emission (left tubein FIG. 11 b). The ratio of total emission from the left tube to thatfrom the right tube was ˜20%; this value is close to the ratio foremission collected with this filter, which is 18%, calculated from theemission spectrum of QD655-Luc8 (FIG. 8 d). These results confirm thatQD655-Luc8-R9 conjugates are functional and produce BRET emission afterbeing taken up into cells.

The QD655-Luc8-R9 labeled cells (˜2×10⁶) were injected via the tail veininto a nude mouse. After subsequent i.v. injection of coelenterazine,the mouse was imaged with and without the long wavelength filter toexamine whether BRET signals from these labeled cells could be detectedin living mice. The left image in FIG. 11 c, collected with thelong-wavelength filter, showed injected cells located in both lungs ofthe mouse. The right image in FIG. 11 c was collected without a filter.The total intensity is approximately the same in both images, suggestingthat the Luc8 emission was significantly scattered and absorbed in deeptissues. A control mouse injected with unlabeled cells did not produceany detectable bioluminescence emission (data not shown).

For comparison, fluorescence spectral imaging of the same mouse wasperformed: only background fluorescence was observed, with no detectableQD fluorescence emission arising from the lungs (FIG. 11 d).Epifluorescence microscopic examination of slices of the sacrificedmouse confirmed the presence of QD655-Luc8 conjugate in the lungs (FIG.11 e). The detection of labeled cells by in vivo bioluminescence QDimaging but not by fluorescence imaging further demonstrates theadvantage of eliminating the need for external excitation and the powerof bioluminescent QDs for imaging studies in living subjects.Fluorescence imaging of QDs requires light to travel in to excite theQDs, and emitted photons to travel out. With bioluminescent QDs,however, no external excitation light is required to travel in to theQDs. By eliminating the need for the excitation light, the surfaceweighting that occurs with traditional reflectance fluorescence imagingsystems is removed, and the issue of background autofluorescence, amajor limiting complication for in vivo fluorescence imaging, iscompletely avoided.

One of the challenges for the use of QDs as in vivo targeting agents isthe relatively large size of these particles. The bioluminescent QDconjugates contain, on average, six copies of immobilized Luc8 with theoverall size of around 20 nm. Surface coating of QDs with high molecularweight polyethylene glycol (PEG) chains has been shown to extend thecirculation time and improve their bioavailability. Furthermodifications of QD-Luc8 conjugates with PEG should further facilitatetheir in vivo tumor targeting.

In summary, this example describes the first example of bioluminescentQD conjugates designed by mimicking the natural BRET process, using amutant of Renilla luciferase as the energy donor and a QD as theacceptor. This example demonstrates that the long wavelength BRETemission can be imaged in both living cells and small living animals.There are several unique features with this system: 1) bothbioluminescence and fluorescence imaging can be performed with ourbioluminescent QDs, combining advantages of both imaging techniques.While conserving the optical properties of QDs, bioluminescent QDs offeran additional advantage over existing QDs: the ability to be imagedwithout external excitation (bioluminescently) results in greatlyenhanced sensitivity in the context of small animal imaging. 2)Bioluminescence emission at longer wavelengths (from 655 nm tonear-infrared 800 nm) than any current bioluminescence probe is readilyavailable by choosing appropriate QDs. These long wavelength emissionsare more easily detected, especially in deep tissues. 3) In vivomultiplexed bioluminescence imaging of multiple targets can be performedby using multiple QD conjugates with distinct BRET emission spectra.These unique features of bioluminescent QD probes should open many newavenues for QD-based imaging, including bioluminescence-based, highlysensitive in vitro assays of multiple targets, cell labeling, in vivocell trafficking, tumor imaging, in vivo multiplexed imaging, and eventhe design of QD-based biosensors where the BRET emission is modulatedby specific biological interactions of interest.

Materials and Methods:

Materials: Quantum dots were purchased from Quantum Dot Corp. (Hayward,Calif.). QD605 and QD655 have typical CdSe/ZnS core-shell structures,and QD705 and QD800 are made of CdTe cores with ZnS coatings. Theorganic coating chemistry has been previously described in theliterature, and the final coated QDs are endowed with carboxylategroups. The quantum yields of each QD determined in 50 mM borate buffer(pH 9) are 65% (QD605), 83% (QD655), 80% (QD705), and 43% (QD800). Thehydrodynamic diameters of all QDs and conjugates were measured with aZetasizer Nano ZS and performed by Malvern Instruments Ltd.(Southborough, Mass.). The coupling reagent1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) wasobtained from Fluka. Coelenterazine, the substrate for Luc8, waspurchased from Prolume (Pinetop, Ariz.). All other chemicals andsolvents were from Sigma-Aldrich. Nude mice (4-6 weeks old) werepurchased from Charles River Breeding Laboratories. Water was purifiedwith Milli-Q biocel (Millipore Corp.). Fluorescence and bioluminescenceemission spectra were collected with a Fluoro Max-3 (JOBIN YVON Inc.,New Jersey); in the case of bioluminescence, the excitation light wasblocked, and emission spectra were corrected with a correction fileprovided by the company. The bioluminescence emission spectra collectedwith the spectrofluorometer were further corrected for the Luc8 kineticsover the course of data acquisition (typically ˜20 s). The enzymaticactivity of Luc8 was measured with a 20/20^(n) Luminometer (TurnerBiosystems, Inc.). Animal fluorescence imaging was carried out with aMaestro imaging system (Cambridge Research & Instrumentation, Inc.).Animal bioluminescence imaging was performed with a Xenogen IVIS 200(Xenogen Corp.). Animal use protocols were reviewed and approved by theInstitutional Animal Care Use Committee of Stanford University.

Preparation of QD and Luc8 conjugates: To a mixture of 8.2 pmol of QDand 164 pmol of Luc8 (20 equivalents) in 200 μL borate buffer (pH=7.4)was added of 32.8 nmol of EDC (4,000 equivalents) (Borate buffer waschosen to minimize QD aggregation during the coupling). The mixture wasincubated for 1 h, and the uncoupled free Luc8 and excess EDC wereremoved by 3 washes in 100K NanoSep filter (Pall Corporation, New York)by centrifugation at 5000 rpm for 3 min at 4° C. The final complex waskept in borate buffer (pH=7.4) at 4° C.

Gel electrophoresis: 1.0 pmol of QD655-Luc8 complex, QD655, and thereaction mixture of QD655 and EDC, with 6× loading dye was run on a 0.5%agarose gel at 100 V in TAE buffer (0.5×).

Cell labeling with QD-Luc8-R9: 8.2 pmol of QD655-Luc8 was activated by1,000 1.64 nmol of EDC (1,000 equivalents) for 5 min. Then 1.64 nmol ofpeptide R9 (200 equivalents) was added, and the mixture was incubatedfor 30 min. The conjugated product was purified by washing andcentrifugation. C6 rat glioma cells were cultured in Dulbecco's ModifiedEagle Medium supplemented with 10% (vol/vol) fetal bovine serum (Gibco)and 1% antibiotic-antimycotic mixture (Gibco). Before incubation with QDconjugates, the culture media were replaced by Hank's Balanced SaltSolution (HBSS). After incubation with QD-Luc8-R9 (1 ml, 10 nM) at 37°C. for 1 h, cells were washed with HBSS 3 times and imaged with aninverted fluorescence microscope (Axiovert 200M, Zeiss). The followingfilter set (Chroma Technology Corporation) was used for QD655 analysis:excitation, 420/40; emission, D660/40; dichroic, 475DCXR. Acquisitiontime: 50 ms, and 40× magnification. For the bioluminescence imaging oflabeled cells, cells were collected by trypsinization or cell scrapers,and suspended in 50 μL of HBSS. After addition of 2 μg ofcoelenterazine, cells were imaged immediately with an IVIS 200bioluminescence imager with and without filter (30 s for eachacquisition).

In vivo bioluminescence imaging: QD conjugates (or labeled cells) wereinjected either subcutaneously, intramuscularly or via tail-vein intonude mice. Mice were subsequently anesthesized with isofluorane, andtransferred into the light-tight chamber of an IVIS 200 imager. After 10min, coelenterazine (10 μg/mouse in 100 μL buffer) was injected i.v. Theimages were acquired with and without filters. Each single acquisitiontook 30 s (for injected QD conjugates) or 2 min (for labeled cells). Tocorrect for the relatively fast in vivo pharmacokinetics ofcoelenterazine, the images were acquired sequentially: 1) with filter(30 s); 2) without filter (30 s); 3) without filter (30 s); 4) withfilter (30 s). The emission with filter was calculated from the averageof 1 and 4, and the emission without filter was the average of 2 and 3.

In vivo fluorescence imaging: Wavelength-resolved spectral imaging wascarried out by using a spectral imaging system (Maestro™ In-Vivo ImagingSystem from Cambridge Research & Instrumentation, Inc. (CRi)) includingan optical head that includes a liquid crystal tunable filter, anoptical coupler, and a CCD camera, along with image acquisition andanalysis software. Excitation filter was 503-555 nm. The tunable filterwas automatically stepped in 10-nm increments from 580 to 900 nm with anexposure time of 49 ms for images captured at each wavelength. Animalswere placed supine under isofluorane anesthesia in a light-tightchamber. Collected images were analyzed by the Maestro software, whichuses spectral unmixing algorithms to remove autofluorescence from the QDsignals. The in vitro multiplexing bioluminescence imaging of QDconjugates was performed similarly with the Maestro system, but with theexcitation light blocked and 5 s exposure time for each individualacquisition.

Histology. Nude mice were sacrificed 1 h and 20 min after injection ofQD-labeled cells. Lungs were collected, washed with PBS, frozen inisopropanol with liquid nitrogen, and kept at −80° C. over night. Frozensamples were microtome sectioned at a thickness of 10 μm. Slides wereanalyzed under a Zeiss inverted fluorescence microscope with the same QDfilter set as described above (objective: 20×; acquisition time: 1 s).

Example 3 Discussion:

Semiconductor quantum dots (QDs) are bright fluorescent emitters withhigh quantum yield, high molar extinction coefficients, size-dependenttunable emission, and high photostability. These attractive fluorescentproperties prompt a wide interest in developing QD-based sensors forbiological detection and imaging. One strategy towards the developmentof QD-based nanosensors is based on fluorescence resonance energytransfer (FRET) with the QDs as the FRET donor. There are numerousexamples of FRET-based QD biosensors including self-assemblednanocomplexes for detecting maltose, pH, 2,4,6-trinitrotoluene,thrombin, and enzyme activity. In these FRET-based QD nanosenors,multiple copies of the FRET acceptor were often present on one QD, whichmay result in the self-quenching and lead to low emission from the FRETacceptor.

Matrix metalloproteinases (MMPs) are a family of zinc-dependent secretedendopeptidases crucial for regulated degradation and processing ofextracellular matrices, and are upregulated in almost every type ofhuman cancers. The significant role of MMPs in promoting cancerprogression makes them important targets for drug development and invivo tumor detection. Fluorescence and magnetic resonance-basedapproaches have been used to detect MMPs activity. This exampledescribes a BRET-based QD nanosensor to detect the activity ofgelatinase MMP-2 with high sensitivity.

The gelatinase MMP-2 has been identified as one of the key MMPs indegrading type-IV collagen. The design of a BRET-based QD sensor for thedetection of the MMP-2 activity is shown in FIG. 15. MMP-2 hydrolyzesthe peptide substrate containing an amino acid sequence of PLGVR. PLGVRcan be fused to the C-terminus of the BRET donor, a mutant of Renillaluciferase (Luc8) without affecting the activity of Luc8. In addition, a6xHis tag was added to the C terminus after PLGVR. In this example,commercially available QDs were used with carboxylic acids presented atthe surface, QD@COOH. In the presence of Ni²⁺, the carboxylic acids onthe QDs will bind the metal ions and form complexes with the 6xHis tagon the Luc8 fusion protein (FIG. 15). The BRET will take place andproduce light emission from the QDs. The cleavage of PLGVR by MMP-2 willrelease the 6xHis tag from the fusion Luc8 and disrupt the BRET (FIG.15).

The efficiency of the Ni²⁺-induced BRET between the QDs and the Luc8fusion protein was first evaluated. When QD655@COOH (50 nM) was mixedwith the fusion protein (400 nM) in the absence of Ni²⁺, upon theaddition of the substrate of Luc8 coelenterazine (1 μg), there was alarge emission from Luc8 at 480 nm but only a small emission from theQDs at 655 nm (<5% of the total emission from Luc8) (FIG. 16). Thissmall peak at 655 nm likely arose from an electrostatic interactionbetween the 6xHis tag on the Luc8 and the negative carboxylate groups onthe QDs. However, when Ni²⁺ (100 μM) was added to the mixture, theemission at 480 nm decreased largely and the emission at 655 nm from theQDs increased significantly, indicating that BRET occurred efficientlybetween the QDs and Luc8. The BRET ratio, defined by the ratio of theintegration of the peak at 655 nm to that of the peak at 480 nm,increased to 1.94.

Both the carboxylate groups on the QDs and the histidine tags on theLuc8 are used for the Ni²⁺-mediated BRET. Addition of an excess amountof EDTA (200 μM), a strong chelator for Ni²⁺, to the mixture containingQD@COOH, the fusion protein and Ni²⁺ greatly decreased the BRET emission(FIG. 16). EDTA competed against the QD@COOH for Ni²⁺ ions, leading tothe dissociation of the QD@COOH and Luc8 complex and, consequently,disrupting the BRET process. When the QDs coated with amino groups(QD655@NH₂) replaced QD655@COOH, no BRET emission from the QDs wasdetected, further confirming that the carboxylate on the QDs are usedfor the binding of Ni²⁺and BRET. When imidazole was added to the mixturecontaining QD@COOH, the Luc8 fusion protein and Ni²⁺, a large decreasein the BRET emission was observed; correspondingly, there was a largeincrease in the Luc8 emission at 480 nm (FIG. 16). These resultsindicate that the interaction between Luc8 and QD@COOH mediated byNi²⁺is specific and dependent on the histidine tag.

After establishing the Ni²⁺-mediated BRET between the QDs and the Luc8fusion protein, these results were applied to the detection of theprotease MMP-2. MMP-2 hydrolyzes the amide bond between the glycine andvaline residues, leading to the cleavage of 6xHis tag from the Luc8fusion protein and the decrease in the BRET ratio. A solution of theLuc8 fusion protein (16 μM in the borate buffer) was incubated withMMP-2 (10 μg/mL) for various periods of time at 22° C., and then wasadded to a solution containing QD@COOH (40 nM) and 100 μM of Ni²⁺for themeasurement of the BRET emission (FIG. 17). Before the MMP-2 cleavage(t=0), there was a strong emission from the QD655 at 655 nm, and theBRET ratio was 1.64. Within 30 minutes, the BRET ratio dropped to 0.62,and the reaction was nearly complete within 2 hours with a BRET ratio of0.21. NuPAGE assay detected a protein product with a smaller size,confirming the hydrolysis by MMP-2.

The sensitivity of this assay was measured with various concentrationsof MMP-2. After 24 hours of incubation at 22° C., the BRET ratiodecreased by ˜20% from 1.6 to 1.3 for a concentration of MMP-2 of 20ng/mL (˜300 pM). The BRET ratio for the control did not change at all.This sensitivity is much higher than reported FRET-based sensors andsimilar to the magnetic sensors.

In comparison to FRET-based QD sensors, BRET-based QD biosensors offerseveral advantages. The spectral separation between the BRET donor andacceptor emission is large, for example, the difference of the maximalemission wavelength in this example is more than 175 nm, which makeseasy to detect both emissions. The sensitivity is high with lowbackground emission. Because of the wide absorption spectra of the QDs,one bioluminescent protein such as Renilla luciferase canefficientlyxcite multiple QDs with different emissions. In theFRET-based QD sensors, several different FRET acceptors are required formultiple QDs with different emissions. Furthermore, the presence ofmultiple copies of the BRET donors on the QD does not decrease butincreases the BRET emission.

In summary, the BRET-based QD biosensing system described here utilizescommercially available carboxylate QDs and a bioluminescent fusionprotein containing a histidine tag and MMP-2 substrate to detect theprotease MMP-2 activity with high sensitivity. This system is simple touse with no need for QD modifications. It offers several advantages overFRET-based sensing mechanism and may serve as a general strategy todesign QD nanosensors for multiplex detection of biological analytes.

Materials and Methods

Preparation of the Luc8 fusion protein: The plasmid Luc8-MMP2-pRSF-Duetwas constructed from plasmid pBAD-RLuc8 by PCR and ligation, the MMP2cleavage site, encoding the amino acid sequence PLGVR, was insertedbetween Luc8 and 6xHis tag. E. Coli BL21 cells transformed with thisplasmid were induced with 0.5 mM IPTG for 3 hours when the opticaldensity at a wavelength of 600 nm (OD₆₀₀) was 0.5. Cells were lysed bythawing in wash buffer solution (WB; 300 mM NaCl, 20 mM2-[4-(2-hydroxyethyl)-1-piperazinyl]ethanesulfonic acid (HEPES), pH8.0), containing lysozyme (1 mg/mL), RNase A (10 μg/mL), and DNaseI (5μg/mL). Lysates were clarified by centrifugation and allowed to bind tonickel affinity resin (Ni-NTA superflow, Qiagen) for 1 h at 4° C. withgentle mixing. After washing with WB, the protein was eluted withelution buffer solution (300 mM NaCl, 20 mM HEPES, pH 8.0, 250 mMimidazole) and further purified by anion-exchange chromatography (Source15Q resin, GE/Amersham) followed by gel-filtration chromatography withborate buffer solution.

MMP-2 assay: A solution of 5 μM of the Luc8 fusion protein in boratebuffer (10 mM CaCl₂, pH 7.5) was incubated with various amounts ofactive human recombinant of MMP-2 (CalBiochem) for a period of time atroom temperature. The BRET measurement was performed by mixingQD655@COOH (40 nM), protein (500 nM) and NiCl₂ (100 μM) in borate buffer(pH 7.5) with Fluoro Max-3 (Jobin Yvon Inc.). Bioluminescence spectrawere acquired with the excitation light blocked. Gel electrophoresisanalysis confirmed the cleavage of the fusion protein by MMP-2. Proteinswere run on a 4-12% Bis-Tris gradient denaturing gel and stained withcommassie blue (FIG. 18).

Comparison of carboxylate QDs and amino QDs for Ni²⁺-mediated BRET: Thecarboxylates on QDs are important for the Ni²⁺-mediated BRET. When theQDs coated with amino groups (QD655@NH₂) replaced QD655@COOH, littleBRET emission from the QDs was detected, further confirming that thecarboxylate groups on the QDs are critical for the binding of Ni²⁺ andBRET (FIG. 19).

Dependence of the BRET emission on [Ni²⁺]: The BRET emission isdependent on the concentration of Ni²⁺. As shown in FIG. 20, with theincrease in the concentration of [Ni²⁺] from 0 to 40 μM, the BRET signalfrom QD kept increasing. Further increase in [Ni²⁺] did not result in anincrease in the BRET ratio, indicating all the QD surface binding siteshave been saturated with the Luc8 fusion protein. Thus in all of ourBRET measurements, 100 μM of [Ni²⁺] was used to ensure the complexformation.

Example 4 Quantum Dot Probes for Multiplexed High Throughput KinaseActivity Assay:

Protein kinase is a family of more than 500 enzymes that facilitate thetransfer of the γ-phosphoryl group of ATP to serine, threonine, andtyrosine residues during protein/peptide phosphorylation. Proteinkinases are found to be critical in both normal physiological processesand variety of diseases including cancer. This example establishes aplatform for a multiplexed high throughput protein kinase activity assayby using quantum dots and bioluminescence proteins. This QD BRET assay,in contrast to the commonly used fluorescence-based methods, has theadvantage of low background and no need for external illumination. Toestablish the assay platform, the Protein Kinase A (PKA) has beenselected as the model target for the system development. FIG. 21illustrates an embodiment of such an assay. In particular, FIG. 21illustrates a schematic of the PKA detection based on the formation ofthe self-illuminating complex mediated by the PKA phosphorylation. Thesubstrate of PKA, kemptide is a short peptide, and can be conjugated toquantum dots (FIG. 21 a) or to the bioluminescent protein such as Luc8(FIG. 21 b). The conjugated kemptide will be phosphorylated in thepresence of ATP by PKA. Phosphorylated kemptides can be detected by aphyspho-specific antibody or metal chelators (such as GaIII) conjugatedto a bioluminescent protein (FIG. 21 a) or to quantum dots (FIG. 21 b).This coupling event brings quantum dots and the bioluminescence proteinto close proximity so as to allow bioluminescence resonance energytransfer (BRET) to occur upon the addition of a substrate. FIG. 22illustrates the result of the PKA detection by the method FIG. 21 b. TheBRET ratio was increased from 0.15 to 0.47 after the PKA phosphorylationof the substrate kemptide.

It should be emphasized that the above-described embodiments of thepresent disclosure are merely possible examples of implementations, andare set forth only for a clear understanding of the principles of thedisclosure. Many variations and modifications may be made to theabove-described embodiments of the disclosure without departingsubstantially from the spirit and principles of the disclosure. All suchmodifications and variations are intended to be included herein withinthe scope of this disclosure and protected by the following claims.

SEQ ID NO: 1 (Rluc) MTSKVYDPEQ RKRMITGPQW WARCKQMNVL DSFINYYDSEKHAENAVIFL HGNAASSYLW RHVVPHIEPV ARCIIPDLIGMGKSGKSGNG SYRLLDHYKY LTAWFELLNL PKKIIFVGHDWGACLAFHYS YEHQDKIKAI VHAESVVDVI ESWDEWPDIEEDIALIKSEE GEKMVLENNF FVETMLPSKI MRKLEPEEFAAYLEPFKEKG EVRRPTLSWP REIPLVKGGK PDVVQIVRNYNAYLRASDDL PKMFIESDPG FFSNAIVEGA KKFPNTEFVKVKGLHFSQED APDEMGKYIK SFVERVLKNE Q SEQ ID NO: 2 (Rluc8)MASKVYDPEQ RKRMITGPQW WARCKQMNVL DSFINYYDSEKHAENAVIFL HGNATSSYLW RHVVPHIEPV ARCIIPDLIGMGKSGKSGNG SYRLLDHYKY LTAWFELLNL PKKIIFVGHDWGAALAFHYA YEHQDRIKAI VHMESVVDVI ESWDEWPDIEEDIALIKSEE GEKMVLENNF FVETVLPSKI MRKLEPEEFAAYLEPFKEKG EVRRPTLSWP REIPLVKGGK PDVVQIVRNYNAYLRASDDL PKLFIESDPG FFSNAIVEGA KKFPNTEFVKVKGLHFLQED APDEMGKYIK SFVERVLKNE Q

1. A conjugate system, comprising: a self-illuminating quantum dotconjugate and a bioluminescence initiating compound, wherein theself-illuminating quantum dot conjugate includes a bioluminescence donormolecule and a quantum dot, wherein the bioluminescence donor moleculeand the bioluminescence initiating compound interact to produce abioluminescence energy, and wherein the quantum dot emits a fluorescenceenergy in response to the non-radiative transfer of the bioluminescenceenergy from the bioluminescence donor molecule to the quantum dot. 2.The system of claim 1, wherein the bioluminescence donor molecule is aLuciferase protein.
 3. The system of claim 1, wherein thebioluminescence donor molecule is selected from a Renilla Luciferaseprotein, a mutated Renilla Luciferase protein, and a combinationthereof.
 4. The system of claim 1, wherein the bioluminescence donormolecule is a mutated Renilla Luciferase protein comprising SEQ ID NO: 2or conservatively modified variants thereof.
 5. The system of claim 1,wherein the self-illuminating quantum dot conjugate includes a firstagent.
 6. The system of claim 5, wherein the first agent has an affinityfor a target, where the target is selected from: a compound, apolypeptide, a polynucleotide, an antibody, an antigen, a hapten, a celltype, a tissue type functional group, a tissue type, and combinationsthereof.
 7. The system of claim 5, wherein the self-illuminating quantumdot conjugate includes a second agent, wherein the second agent iseffective at treating a disease.
 8. The system of claim 1, wherein theself-illuminating quantum dot conjugate includes a second agent, whereinthe second agent is effective at treating a disease.
 9. The system ofclaim 1, wherein the quantum dot comprises a core and a cap.
 10. Thesystem of claim 9, wherein the core of the quantum dot is selected from:IIB-VIB semiconductors, IIIB-VB semiconductors, and IVB-IVBsemiconductors; and wherein the cap is selected from: IIB-VIBsemiconductors of high band gap.
 11. The structure of claim 10, whereinthe core of the quantum dot is selected from CdS and CdSe, and the capis selected from ZnS and CdS.
 12. The system of claim 11, wherein thebioluminescence donor molecule is a Luciferase protein.
 13. The systemof claim 12, wherein the bioluminescence donor molecule is a mutatedRenilla Luciferase protein comprising SEQ ID NO: 2 or conservativelymodified variants thereof.
 14. The system of claim 13, wherein thequantum dot is CdSe/ZnS.
 15. The system of claim 1, wherein thebioluminescence initiating compound is selected from coelenterazine,analogs, and functional derivatives thereof, and D-luciferin analogs,and functional derivatives thereof.
 16. A conjugate system, comprising:a bioluminescence donor molecule and a quantum dot, wherein abioluminescence energy is produced from the bioluminescence donormolecule, and wherein the quantum dot emits a fluorescence energy inresponse to the non-radiative transfer of the bioluminescence energyfrom the bioluminescence donor molecule to the quantum dot.
 17. Theconjugate system of claim 16, wherein the bioluminescence donor moleculeis a Luciferase protein.
 18. The conjugate system of claim 16, whereinat least one of the bioluminescence donor molecule and the quantum dotincludes a first agent.
 19. The conjugate system of claim 18, whereinthe first agent has an affinity for a target, where the target isselected from: a compound, a polypeptide, a polynucleotide, an antibody,an antigen, a hapten, a cell type, a tissue type functional group, atissue type, and combinations thereof.
 20. The conjugate system of claim19, wherein at least one of the bioluminescence donor molecule and thequantum dot includes a second agent, wherein the second agent iseffective at treating a disease.
 21. The conjugate system of claim 16,wherein the quantum dot comprises a core and a cap, wherein the core ofthe quantum dot is selected from: IIB-VIB semiconductors, IIIB-VBsemiconductors, and IVB-IVB semiconductors; and wherein the cap isselected from: IIB-VIB semiconductors of high band gap.
 22. Theconjugate system of claim 1, wherein the quantum dot comprises a quantumdot composite.
 23. A method of detecting a target in a host, comprising:providing a self-illuminating quantum dot conjugate, wherein theself-illuminating quantum dot conjugate includes a bioluminescence donormolecule, a quantum dot, and at least one agent, wherein the agent hasan affinity for the target; introducing the self-illuminating quantumdot conjugate to a host; introducing a bioluminescence initiatingcompound to the host; and determining the presence and location of thetarget in the host corresponding to the agent by detecting theself-illuminating quantum dot conjugate upon interaction with thebioluminescence initiating compound.
 24. The method of claim 23, whereindetermining includes detecting a radiation emission from the quantum dotwithout the use of an external illumination source.
 25. The method ofclaim 23, wherein determining includes determining the presence andlocation of the target in the host in vivo.
 26. The method of claim 23,wherein determining includes determining the presence and location ofthe target in the host in vitro.
 27. The method of claim 23, wherein thetarget is selected from: a compound, a polypeptide, a polynucleotide, anantibody, an antigen, a hapten, a cell type, a tissue type functionalgroup, a tissue type, and combinations thereof.
 28. A method of treatinga disease in a host, comprising: providing a self-illuminating quantumdot conjugate, wherein the self-illuminating quantum dot conjugateincludes a bioluminescence donor molecule, a quantum dot, and a firstagent, wherein the first agent is effective at treating the disease;introducing the self-illuminating quantum dot conjugate to the subjectin need of treatment of the disease; introducing a bioluminescenceinitiating compound to the host; and determining the location of theself-illuminating quantum dot conjugate in the host upon interactionwith the bioluminescence initiating compound.
 29. The method of claim28, wherein determining includes detecting a radiation emission from thequantum dot without the use of an external illumination source.
 30. Themethod of claim 28, wherein the self-illuminating quantum dot conjugateincludes a second agent, wherein the second agent has an affinity for atarget, and wherein the target is associated with the disease.
 31. Themethod of claim 30, further comprising: determining the presence andlocation of the target in the host corresponding to the agent bydetecting the self-illuminating quantum dot conjugate upon interactionwith the bioluminescence initiating compound.
 32. The method of claim31, wherein the target is selected from: a compound, a polypeptide, apolynucleotide, an antibody, an antigen, a hapten, a cell type, a tissuetype functional group, a tissue type, and combinations thereof.
 33. Amethod of detecting a target in a host, comprising: providing aself-illuminating quantum dot conjugate, wherein the self-illuminatingquantum dot conjugate includes a bioluminescence donor molecule, aquantum dot, and a first agent, wherein the first agent is disposedbetween the quantum dot and the bioluminescence donor molecule, andwherein the first agent is degraded by the target; introducing theself-illuminating quantum dot conjugate to a host; introducing abioluminescence initiating compound to the host; detecting a fluorescentenergy emitted from the quantum dot; and determining the presence of thetarget in the host by detecting decay of the fluorescent energy emittedfrom the quantum dot of the self-illuminating quantum dot conjugate upondegradation of the first agent.
 34. A method of detecting a target in asystem, comprising: providing a bioluminescence donor molecule complexand a quantum dot complex, wherein the bioluminescence donor moleculecomplex includes a bioluminescence donor molecule, wherein the quantumdot complex includes a quantum dot; introducing each of thebioluminescence donor molecule complex and the quantum dot complexindependently to the system, wherein if the system includes the target,the target interacts with at least one of the bioluminescence donormolecule complex or the quantum dot complex to cause the bioluminescencedonor molecule complex and the quantum dot complex to becomesubstantially close to one another; introducing a bioluminescenceinitiating compound to the system, wherein the bioluminescence donormolecule and the bioluminescence initiating compound interact to producea bioluminescence energy, and wherein the quantum dot emits afluorescence energy in response to non-radiative transfer of thebioluminescence energy from the bioluminescence donor molecule to thequantum dot; and determining the presence of the target by detecting thefluorescent energy emitted from the quantum dot.
 35. The method of claim34, wherein determining includes determining the presence of the targetin the system in vivo.
 36. The method of claim 34, wherein determiningincludes determining the presence of the target in the system in vitro.37. The method of claim 34, wherein the target activates the combinationof the two complexes.
 38. A method of detecting a target in a system,comprising: providing a bioluminescence donor molecule complex and aquantum dot complex, wherein the bioluminescence donor molecule complexincludes a bioluminescence donor molecule, wherein the quantum dotcomplex includes a quantum dot, wherein one of the bioluminescence donormolecule complex or the quantum dot complex includes a first agent thathas an affinity for the first target, wherein the first target undergoesa change to a second target upon interaction with the first agent,wherein the other of the bioluminescence donor molecule complex or thequantum dot complex includes a second agent that has an affinity for thesecond target; introducing each of the bioluminescence donor moleculecomplex and the quantum dot complex independently to the system, whereinif the system includes the first target the first target undergoes achange to the second target upon interaction with the first agent,wherein the bioluminescence donor molecule complex and the quantum dotcomplex become substantially close to one another upon interaction ofthe third agent with the second target; introducing a bioluminescenceinitiating compound to the system, wherein the bioluminescence donormolecule and the bioluminescence initiating compound interact to producea bioluminescence energy, and wherein the quantum dot emits afluorescence energy in response to the non-radiative transfer of thebioluminescence energy from the bioluminescence donor molecule to thequantum dot; and determining the presence of the second target bydetecting the fluorescent energy emitted from the quantum dot.
 39. Themethod of claim 38, wherein determining includes determining thepresence of the target in the system in vivo.
 40. The method of claim38, wherein determining includes determining the presence of the targetin the system in vitro.
 41. A method of detecting a target in a system,comprising: providing a bioluminescence donor molecule complex and aquantum dot complex, wherein the bioluminescence donor molecule complexincludes a bioluminescence donor molecule, wherein the quantum dotcomplex includes a quantum dot, wherein one of the bioluminescence donormolecule complex or the quantum dot complex includes a first agent thathas an affinity for the first target, wherein the first agent undergoesa change to a second agent upon interaction with the first target,wherein the other of the bioluminescence donor molecule complex or thequantum dot complex includes a third agent that has an affinity for thesecond target; introducing each of the bioluminescence donor moleculecomplex and the quantum dot complex independently to the system, whereinif the system includes the first target the first agent undergoes achange to the second agent upon interaction with the first agent,wherein the bioluminescence donor molecule complex and the quantum dotcomplex become substantially close to one another upon interaction ofthe third agent with the second agent; introducing a bioluminescenceinitiating compound to the system, wherein the bioluminescence donormolecule and the bioluminescence initiating compound interact to producea bioluminescence energy, and wherein the quantum dot emits afluorescence energy in response to the non-radiative transfer of thebioluminescence energy from the bioluminescence donor molecule to thequantum dot; and determining the presence of the second target bydetecting the fluorescent energy emitted from the quantum dot.
 42. Themethod of claim 41, wherein determining includes determining thepresence of the target in the system in vivo.
 43. The method of claim41, wherein determining includes determining the presence of the targetin the system in vitro.